[{"data":1,"prerenderedAt":1258},["ShallowReactive",2],{"mdc--2k2qpd-key":3},{"data":4,"body":5},{},{"type":6,"children":7},"root",[8,24,39,43,50,67,72,102,105,111,161,166,178,183,194,197,203,210,264,269,284,287,293,335,338,344,349,367,372,380,385,400,405,420,423,429,434,446,449,456,462,467,473,478,491,497,502,510,513,519,545,555,558,564,569,580,673,678,683,701,704,710,715,720,725,748,753,771,776,779,785,790,796,818,824,847,852,870,873,879,885,890,903,908,926,929,935,946,951,965,970,978,981,987,992,997,1016,1021,1024,1030,1036,1041,1049,1052,1058,1063,1081,1086,1091,1094,1100,1105,1128,1133,1141,1144,1150,1161,1179,1184,1192,1197,1200,1206,1211,1216,1219,1225,1235],{"type":9,"tag":10,"props":11,"children":12},"element","p",{},[13,16,22],{"type":14,"value":15},"text","Here is a ",{"type":9,"tag":17,"props":18,"children":19},"strong",{},[20],{"type":14,"value":21},"fun, structured, and educational deep summary",{"type":14,"value":23}," of the review article:",{"type":9,"tag":25,"props":26,"children":27},"blockquote",{},[28],{"type":9,"tag":10,"props":29,"children":30},{},[31,33],{"type":14,"value":32},"** – ",{"type":9,"tag":34,"props":35,"children":36},"em",{},[37],{"type":14,"value":38},"Protein crystallography for non-crystallographers (Wlodawer et al., 2008)",{"type":9,"tag":40,"props":41,"children":42},"hr",{},[],{"type":9,"tag":44,"props":45,"children":47},"h1",{"id":46},"protein-crystallography-for-non-crystallographers-detailed-summary",[48],{"type":14,"value":49},"🧬 Protein Crystallography for Non-Crystallographers — Detailed Summary",{"type":9,"tag":10,"props":51,"children":52},{},[53,55,60,62],{"type":14,"value":54},"This review is essentially a ",{"type":9,"tag":17,"props":56,"children":57},{},[58],{"type":14,"value":59},"survival guide for biologists / structural users",{"type":14,"value":61}," who download PDB structures and want to ",{"type":9,"tag":17,"props":63,"children":64},{},[65],{"type":14,"value":66},"interpret them correctly — without over-interpreting them.",{"type":9,"tag":10,"props":68,"children":69},{},[70],{"type":14,"value":71},"It explains:",{"type":9,"tag":73,"props":74,"children":75},"ul",{},[76,82,87,92,97],{"type":9,"tag":77,"props":78,"children":79},"li",{},[80],{"type":14,"value":81},"How crystal structures are determined",{"type":9,"tag":77,"props":83,"children":84},{},[85],{"type":14,"value":86},"What electron density actually means",{"type":9,"tag":77,"props":88,"children":89},{},[90],{"type":14,"value":91},"How to judge structure quality",{"type":9,"tag":77,"props":93,"children":94},{},[95],{"type":14,"value":96},"Common mistakes and red flags",{"type":9,"tag":77,"props":98,"children":99},{},[100],{"type":14,"value":101},"How to interpret biological conclusions safely",{"type":9,"tag":40,"props":103,"children":104},{},[],{"type":9,"tag":44,"props":106,"children":108},{"id":107},"why-protein-crystal-structures-matter",[109],{"type":14,"value":110},"🌍 Why Protein Crystal Structures Matter",{"type":9,"tag":73,"props":112,"children":113},{},[114,126,138],{"type":9,"tag":77,"props":115,"children":116},{},[117,119,124],{"type":14,"value":118},"The ",{"type":9,"tag":17,"props":120,"children":121},{},[122],{"type":14,"value":123},"Protein Data Bank (PDB)",{"type":14,"value":125}," contains tens of thousands of macromolecular structures.",{"type":9,"tag":77,"props":127,"children":128},{},[129,131,136],{"type":14,"value":130},"Most are solved by ",{"type":9,"tag":17,"props":132,"children":133},{},[134],{"type":14,"value":135},"X-ray crystallography",{"type":14,"value":137},".",{"type":9,"tag":77,"props":139,"children":140},{},[141,143],{"type":14,"value":142},"Structural information is crucial for:",{"type":9,"tag":73,"props":144,"children":145},{},[146,151,156],{"type":9,"tag":77,"props":147,"children":148},{},[149],{"type":14,"value":150},"Understanding biological mechanisms",{"type":9,"tag":77,"props":152,"children":153},{},[154],{"type":14,"value":155},"Drug design",{"type":9,"tag":77,"props":157,"children":158},{},[159],{"type":14,"value":160},"Protein engineering",{"type":9,"tag":10,"props":162,"children":163},{},[164],{"type":14,"value":165},"BUT:",{"type":9,"tag":10,"props":167,"children":168},{},[169,171,176],{"type":14,"value":170},"👉 Beautiful molecular graphics can be misleading.\n👉 Coordinates are ",{"type":9,"tag":17,"props":172,"children":173},{},[174],{"type":14,"value":175},"interpretations of experimental data",{"type":14,"value":177},", not direct observations.",{"type":9,"tag":10,"props":179,"children":180},{},[181],{"type":14,"value":182},"The paper’s core message:",{"type":9,"tag":25,"props":184,"children":185},{},[186],{"type":9,"tag":10,"props":187,"children":188},{},[189],{"type":9,"tag":17,"props":190,"children":191},{},[192],{"type":14,"value":193},"Users must learn to critically evaluate structures — not just trust them.",{"type":9,"tag":40,"props":195,"children":196},{},[],{"type":9,"tag":44,"props":198,"children":200},{"id":199},"how-a-crystal-structure-is-determined-conceptual-workflow",[201],{"type":14,"value":202},"🔬 How a Crystal Structure Is Determined (Conceptual Workflow)",{"type":9,"tag":204,"props":205,"children":207},"h3",{"id":206},"_1️⃣-x-ray-diffraction",[208],{"type":14,"value":209},"1️⃣ X-ray diffraction",{"type":9,"tag":73,"props":211,"children":212},{},[213,224,235,253],{"type":9,"tag":77,"props":214,"children":215},{},[216,218,223],{"type":14,"value":217},"X-rays scatter off ",{"type":9,"tag":17,"props":219,"children":220},{},[221],{"type":14,"value":222},"electrons in atoms",{"type":14,"value":137},{"type":9,"tag":77,"props":225,"children":226},{},[227,229,234],{"type":14,"value":228},"A crystal behaves like a ",{"type":9,"tag":17,"props":230,"children":231},{},[232],{"type":14,"value":233},"3D diffraction grating",{"type":14,"value":137},{"type":9,"tag":77,"props":236,"children":237},{},[238,240],{"type":14,"value":239},"The geometry of diffraction spots depends on:",{"type":9,"tag":73,"props":241,"children":242},{},[243,248],{"type":9,"tag":77,"props":244,"children":245},{},[246],{"type":14,"value":247},"Crystal lattice",{"type":9,"tag":77,"props":249,"children":250},{},[251],{"type":14,"value":252},"Wavelength",{"type":9,"tag":77,"props":254,"children":255},{},[256,257,262],{"type":14,"value":118},{"type":9,"tag":17,"props":258,"children":259},{},[260],{"type":14,"value":261},"intensity",{"type":14,"value":263}," depends on atom positions.",{"type":9,"tag":10,"props":265,"children":266},{},[267],{"type":14,"value":268},"Important insight:",{"type":9,"tag":25,"props":270,"children":271},{},[272],{"type":9,"tag":10,"props":273,"children":274},{},[275,277,282],{"type":14,"value":276},"Each reflection depends on the positions of ",{"type":9,"tag":17,"props":278,"children":279},{},[280],{"type":14,"value":281},"all atoms",{"type":14,"value":283},", so the entire structure must be modeled.",{"type":9,"tag":40,"props":285,"children":286},{},[],{"type":9,"tag":204,"props":288,"children":290},{"id":289},"_2️⃣-phase-problem",[291],{"type":14,"value":292},"2️⃣ Phase problem",{"type":9,"tag":73,"props":294,"children":295},{},[296,307,325],{"type":9,"tag":77,"props":297,"children":298},{},[299,301,306],{"type":14,"value":300},"Diffraction gives ",{"type":9,"tag":17,"props":302,"children":303},{},[304],{"type":14,"value":305},"amplitudes but not phases",{"type":14,"value":137},{"type":9,"tag":77,"props":308,"children":309},{},[310,312],{"type":14,"value":311},"Phases must be obtained via methods like:",{"type":9,"tag":73,"props":313,"children":314},{},[315,320],{"type":9,"tag":77,"props":316,"children":317},{},[318],{"type":14,"value":319},"Molecular replacement",{"type":9,"tag":77,"props":321,"children":322},{},[323],{"type":14,"value":324},"Heavy atom methods",{"type":9,"tag":77,"props":326,"children":327},{},[328,330],{"type":14,"value":329},"Initial phases → ",{"type":9,"tag":17,"props":331,"children":332},{},[333],{"type":14,"value":334},"approximate electron density map",{"type":9,"tag":40,"props":336,"children":337},{},[],{"type":9,"tag":204,"props":339,"children":341},{"id":340},"_3️⃣-model-building-refinement",[342],{"type":14,"value":343},"3️⃣ Model building + refinement",{"type":9,"tag":10,"props":345,"children":346},{},[347],{"type":14,"value":348},"Refinement adjusts:",{"type":9,"tag":73,"props":350,"children":351},{},[352,357,362],{"type":9,"tag":77,"props":353,"children":354},{},[355],{"type":14,"value":356},"Atomic coordinates (x,y,z)",{"type":9,"tag":77,"props":358,"children":359},{},[360],{"type":14,"value":361},"B-factor (atomic mobility / disorder)",{"type":9,"tag":77,"props":363,"children":364},{},[365],{"type":14,"value":366},"Occupancy",{"type":9,"tag":10,"props":368,"children":369},{},[370],{"type":14,"value":371},"Optimization aims to:",{"type":9,"tag":73,"props":373,"children":374},{},[375],{"type":9,"tag":77,"props":376,"children":377},{},[378],{"type":14,"value":379},"Minimize difference between observed and calculated diffraction.",{"type":9,"tag":10,"props":381,"children":382},{},[383],{"type":14,"value":384},"⚠️ Huge complexity:",{"type":9,"tag":73,"props":386,"children":387},{},[388],{"type":9,"tag":77,"props":389,"children":390},{},[391,393,398],{"type":14,"value":392},"Even a ",{"type":9,"tag":17,"props":394,"children":395},{},[396],{"type":14,"value":397},"20 kDa protein ≈ 6000 parameters",{"type":14,"value":399}," to refine.",{"type":9,"tag":10,"props":401,"children":402},{},[403],{"type":14,"value":404},"Hence:",{"type":9,"tag":73,"props":406,"children":407},{},[408],{"type":9,"tag":77,"props":409,"children":410},{},[411,413,418],{"type":14,"value":412},"Refinement uses ",{"type":9,"tag":17,"props":414,"children":415},{},[416],{"type":14,"value":417},"stereochemical restraints",{"type":14,"value":419}," (chemical knowledge).",{"type":9,"tag":40,"props":421,"children":422},{},[],{"type":9,"tag":44,"props":424,"children":426},{"id":425},"️-electron-density-maps-the-real-experimental-result",[427],{"type":14,"value":428},"🗺️ Electron Density Maps — The Real Experimental Result",{"type":9,"tag":10,"props":430,"children":431},{},[432],{"type":14,"value":433},"Important conceptual point:",{"type":9,"tag":25,"props":435,"children":436},{},[437],{"type":9,"tag":10,"props":438,"children":439},{},[440,441],{"type":14,"value":118},{"type":9,"tag":17,"props":442,"children":443},{},[444],{"type":14,"value":445},"electron density map is the experiment.\nThe atomic model is interpretation.",{"type":9,"tag":40,"props":447,"children":448},{},[],{"type":9,"tag":450,"props":451,"children":453},"h2",{"id":452},"types-of-maps",[454],{"type":14,"value":455},"Types of maps",{"type":9,"tag":204,"props":457,"children":459},{"id":458},"fobs-φcalc-map",[460],{"type":14,"value":461},"🟦 (Fobs, φcalc) map",{"type":9,"tag":10,"props":463,"children":464},{},[465],{"type":14,"value":466},"→ Approximate structure density.",{"type":9,"tag":204,"props":468,"children":470},{"id":469},"difference-map-fobs-fcalc",[471],{"type":14,"value":472},"🟥 Difference map (Fobs − Fcalc)",{"type":9,"tag":10,"props":474,"children":475},{},[476],{"type":14,"value":477},"Shows:",{"type":9,"tag":73,"props":479,"children":480},{},[481,486],{"type":9,"tag":77,"props":482,"children":483},{},[484],{"type":14,"value":485},"Positive peaks → missing atoms",{"type":9,"tag":77,"props":487,"children":488},{},[489],{"type":14,"value":490},"Negative peaks → wrongly modeled atoms",{"type":9,"tag":204,"props":492,"children":494},{"id":493},"_2fobs-fcalc-map",[495],{"type":14,"value":496},"🟩 2Fobs − Fcalc map",{"type":9,"tag":10,"props":498,"children":499},{},[500],{"type":14,"value":501},"Most commonly used:",{"type":9,"tag":73,"props":503,"children":504},{},[505],{"type":9,"tag":77,"props":506,"children":507},{},[508],{"type":14,"value":509},"Combines both for visualization.",{"type":9,"tag":40,"props":511,"children":512},{},[],{"type":9,"tag":450,"props":514,"children":516},{"id":515},"noise-and-contour-levels",[517],{"type":14,"value":518},"Noise and contour levels",{"type":9,"tag":73,"props":520,"children":521},{},[522,527],{"type":9,"tag":77,"props":523,"children":524},{},[525],{"type":14,"value":526},"Maps contain noise due to experimental errors.",{"type":9,"tag":77,"props":528,"children":529},{},[530,532],{"type":14,"value":531},"Typical contour levels:",{"type":9,"tag":73,"props":533,"children":534},{},[535,540],{"type":9,"tag":77,"props":536,"children":537},{},[538],{"type":14,"value":539},"~1σ for main map",{"type":9,"tag":77,"props":541,"children":542},{},[543],{"type":14,"value":544},"±3σ for difference map",{"type":9,"tag":10,"props":546,"children":547},{},[548,550],{"type":14,"value":549},"Using lower levels can ",{"type":9,"tag":17,"props":551,"children":552},{},[553],{"type":14,"value":554},"show noise instead of real structure.",{"type":9,"tag":40,"props":556,"children":557},{},[],{"type":9,"tag":44,"props":559,"children":561},{"id":560},"resolution-the-most-important-parameter",[562],{"type":14,"value":563},"📏 Resolution — The Most Important Parameter",{"type":9,"tag":10,"props":565,"children":566},{},[567],{"type":14,"value":568},"Resolution determines:",{"type":9,"tag":25,"props":570,"children":571},{},[572],{"type":9,"tag":10,"props":573,"children":574},{},[575],{"type":9,"tag":17,"props":576,"children":577},{},[578],{"type":14,"value":579},"Level of detail visible in the structure.",{"type":9,"tag":581,"props":582,"children":583},"table",{},[584,603],{"type":9,"tag":585,"props":586,"children":587},"thead",{},[588],{"type":9,"tag":589,"props":590,"children":591},"tr",{},[592,598],{"type":9,"tag":593,"props":594,"children":595},"th",{},[596],{"type":14,"value":597},"Resolution",{"type":9,"tag":593,"props":599,"children":600},{},[601],{"type":14,"value":602},"What you see",{"type":9,"tag":604,"props":605,"children":606},"tbody",{},[607,621,634,647,660],{"type":9,"tag":589,"props":608,"children":609},{},[610,616],{"type":9,"tag":611,"props":612,"children":613},"td",{},[614],{"type":14,"value":615},"~6 Å",{"type":9,"tag":611,"props":617,"children":618},{},[619],{"type":14,"value":620},"Overall shape",{"type":9,"tag":589,"props":622,"children":623},{},[624,629],{"type":9,"tag":611,"props":625,"children":626},{},[627],{"type":14,"value":628},"~3 Å",{"type":9,"tag":611,"props":630,"children":631},{},[632],{"type":14,"value":633},"Secondary structure",{"type":9,"tag":589,"props":635,"children":636},{},[637,642],{"type":9,"tag":611,"props":638,"children":639},{},[640],{"type":14,"value":641},"~2 Å",{"type":9,"tag":611,"props":643,"children":644},{},[645],{"type":14,"value":646},"Side chains + waters",{"type":9,"tag":589,"props":648,"children":649},{},[650,655],{"type":9,"tag":611,"props":651,"children":652},{},[653],{"type":14,"value":654},"~1.2 Å",{"type":9,"tag":611,"props":656,"children":657},{},[658],{"type":14,"value":659},"Atomic resolution",{"type":9,"tag":589,"props":661,"children":662},{},[663,668],{"type":9,"tag":611,"props":664,"children":665},{},[666],{"type":14,"value":667},"\u003C1 Å",{"type":9,"tag":611,"props":669,"children":670},{},[671],{"type":14,"value":672},"Hydrogen atoms",{"type":9,"tag":10,"props":674,"children":675},{},[676],{"type":14,"value":677},"Higher resolution → more reflections → better model.",{"type":9,"tag":10,"props":679,"children":680},{},[681],{"type":14,"value":682},"At atomic resolution:",{"type":9,"tag":73,"props":684,"children":685},{},[686,691,696],{"type":9,"tag":77,"props":687,"children":688},{},[689],{"type":14,"value":690},"Individual peaks separate",{"type":9,"tag":77,"props":692,"children":693},{},[694],{"type":14,"value":695},"Atom types distinguishable",{"type":9,"tag":77,"props":697,"children":698},{},[699],{"type":14,"value":700},"Unusual conformations detectable.",{"type":9,"tag":40,"props":702,"children":703},{},[],{"type":9,"tag":44,"props":705,"children":707},{"id":706},"disorder-and-solvent",[708],{"type":14,"value":709},"💧 Disorder and Solvent",{"type":9,"tag":10,"props":711,"children":712},{},[713],{"type":14,"value":714},"Protein crystals are:",{"type":9,"tag":10,"props":716,"children":717},{},[718],{"type":14,"value":719},"👉 ~50% solvent on average.",{"type":9,"tag":10,"props":721,"children":722},{},[723],{"type":14,"value":724},"Two disorder types:",{"type":9,"tag":73,"props":726,"children":727},{},[728,738],{"type":9,"tag":77,"props":729,"children":730},{},[731,736],{"type":9,"tag":17,"props":732,"children":733},{},[734],{"type":14,"value":735},"Static disorder",{"type":14,"value":737}," — multiple conformations",{"type":9,"tag":77,"props":739,"children":740},{},[741,746],{"type":9,"tag":17,"props":742,"children":743},{},[744],{"type":14,"value":745},"Dynamic disorder",{"type":14,"value":747}," — atomic motion",{"type":9,"tag":10,"props":749,"children":750},{},[751],{"type":14,"value":752},"Consequences:",{"type":9,"tag":73,"props":754,"children":755},{},[756,761,766],{"type":9,"tag":77,"props":757,"children":758},{},[759],{"type":14,"value":760},"Density smearing",{"type":9,"tag":77,"props":762,"children":763},{},[764],{"type":14,"value":765},"Poor modeling in flexible regions",{"type":9,"tag":77,"props":767,"children":768},{},[769],{"type":14,"value":770},"Missing density in low-resolution maps",{"type":9,"tag":10,"props":772,"children":773},{},[774],{"type":14,"value":775},"Water modeling depends strongly on resolution.",{"type":9,"tag":40,"props":777,"children":778},{},[],{"type":9,"tag":44,"props":780,"children":782},{"id":781},"what-to-check-in-a-pdb-file-practical-guide",[783],{"type":14,"value":784},"🧾 What to Check in a PDB File (Practical Guide)",{"type":9,"tag":10,"props":786,"children":787},{},[788],{"type":14,"value":789},"Always inspect:",{"type":9,"tag":204,"props":791,"children":793},{"id":792},"data-quality-indicators",[794],{"type":14,"value":795},"📊 Data quality indicators",{"type":9,"tag":73,"props":797,"children":798},{},[799,803,808,813],{"type":9,"tag":77,"props":800,"children":801},{},[802],{"type":14,"value":597},{"type":9,"tag":77,"props":804,"children":805},{},[806],{"type":14,"value":807},"Completeness",{"type":9,"tag":77,"props":809,"children":810},{},[811],{"type":14,"value":812},"I/σ(I) (signal-to-noise)",{"type":9,"tag":77,"props":814,"children":815},{},[816],{"type":14,"value":817},"Rmerge",{"type":9,"tag":204,"props":819,"children":821},{"id":820},"model-quality-indicators",[822],{"type":14,"value":823},"🧱 Model quality indicators",{"type":9,"tag":73,"props":825,"children":826},{},[827,832,837,842],{"type":9,"tag":77,"props":828,"children":829},{},[830],{"type":14,"value":831},"R-factor",{"type":9,"tag":77,"props":833,"children":834},{},[835],{"type":14,"value":836},"Rfree",{"type":9,"tag":77,"props":838,"children":839},{},[840],{"type":14,"value":841},"Geometry deviations",{"type":9,"tag":77,"props":843,"children":844},{},[845],{"type":14,"value":846},"Ramachandran plot",{"type":9,"tag":10,"props":848,"children":849},{},[850],{"type":14,"value":851},"PDB headers may be:",{"type":9,"tag":73,"props":853,"children":854},{},[855,860,865],{"type":9,"tag":77,"props":856,"children":857},{},[858],{"type":14,"value":859},"incomplete",{"type":9,"tag":77,"props":861,"children":862},{},[863],{"type":14,"value":864},"contradictory",{"type":9,"tag":77,"props":866,"children":867},{},[868],{"type":14,"value":869},"even erroneous.",{"type":9,"tag":40,"props":871,"children":872},{},[],{"type":9,"tag":44,"props":874,"children":876},{"id":875},"r-factor-and-rfree-structure-quality-metrics",[877],{"type":14,"value":878},"📉 R-factor and Rfree — Structure Quality Metrics",{"type":9,"tag":204,"props":880,"children":882},{"id":881},"r-factor",[883],{"type":14,"value":884},"🔵 R-factor",{"type":9,"tag":10,"props":886,"children":887},{},[888],{"type":14,"value":889},"Measures agreement between:",{"type":9,"tag":73,"props":891,"children":892},{},[893,898],{"type":9,"tag":77,"props":894,"children":895},{},[896],{"type":14,"value":897},"Observed diffraction",{"type":9,"tag":77,"props":899,"children":900},{},[901],{"type":14,"value":902},"Model diffraction",{"type":9,"tag":10,"props":904,"children":905},{},[906],{"type":14,"value":907},"Guidelines:",{"type":9,"tag":73,"props":909,"children":910},{},[911,916,921],{"type":9,"tag":77,"props":912,"children":913},{},[914],{"type":14,"value":915},"Good: \u003C20%",{"type":9,"tag":77,"props":917,"children":918},{},[919],{"type":14,"value":920},"Suspicious: ~30%",{"type":9,"tag":77,"props":922,"children":923},{},[924],{"type":14,"value":925},"Excellent: \u003C10%",{"type":9,"tag":40,"props":927,"children":928},{},[],{"type":9,"tag":204,"props":930,"children":932},{"id":931},"rfree",[933],{"type":14,"value":934},"🟠 Rfree",{"type":9,"tag":10,"props":936,"children":937},{},[938,940,945],{"type":14,"value":939},"Calculated on ",{"type":9,"tag":17,"props":941,"children":942},{},[943],{"type":14,"value":944},"unused reflections",{"type":14,"value":137},{"type":9,"tag":10,"props":947,"children":948},{},[949],{"type":14,"value":950},"Purpose:",{"type":9,"tag":73,"props":952,"children":953},{},[954],{"type":9,"tag":77,"props":955,"children":956},{},[957,959,964],{"type":14,"value":958},"Detect ",{"type":9,"tag":17,"props":960,"children":961},{},[962],{"type":14,"value":963},"over-fitting",{"type":14,"value":137},{"type":9,"tag":10,"props":966,"children":967},{},[968],{"type":14,"value":969},"Warning signs:",{"type":9,"tag":73,"props":971,"children":972},{},[973],{"type":9,"tag":77,"props":974,"children":975},{},[976],{"type":14,"value":977},"Rfree − R > 7% → possible over-interpretation.",{"type":9,"tag":40,"props":979,"children":980},{},[],{"type":9,"tag":44,"props":982,"children":984},{"id":983},"geometry-validation",[985],{"type":14,"value":986},"📐 Geometry Validation",{"type":9,"tag":450,"props":988,"children":990},{"id":989},"ramachandran-plot",[991],{"type":14,"value":846},{"type":9,"tag":10,"props":993,"children":994},{},[995],{"type":14,"value":996},"Shows backbone torsion angles.",{"type":9,"tag":73,"props":998,"children":999},{},[1000,1011],{"type":9,"tag":77,"props":1001,"children":1002},{},[1003],{"type":9,"tag":25,"props":1004,"children":1005},{},[1006],{"type":9,"tag":10,"props":1007,"children":1008},{},[1009],{"type":14,"value":1010},"90% residues in favored regions → good structure",{"type":9,"tag":77,"props":1012,"children":1013},{},[1014],{"type":14,"value":1015},"Many outliers → major issues",{"type":9,"tag":10,"props":1017,"children":1018},{},[1019],{"type":14,"value":1020},"Peptide planarity and bond rmsd also critical.",{"type":9,"tag":40,"props":1022,"children":1023},{},[],{"type":9,"tag":44,"props":1025,"children":1027},{"id":1026},"️-common-problems-in-published-structures",[1028],{"type":14,"value":1029},"⚠️ Common Problems in Published Structures",{"type":9,"tag":450,"props":1031,"children":1033},{"id":1032},"_1️⃣-fabrication-or-manipulation-rare",[1034],{"type":14,"value":1035},"1️⃣ Fabrication or manipulation (rare)",{"type":9,"tag":10,"props":1037,"children":1038},{},[1039],{"type":14,"value":1040},"Example:",{"type":9,"tag":73,"props":1042,"children":1043},{},[1044],{"type":9,"tag":77,"props":1045,"children":1046},{},[1047],{"type":14,"value":1048},"Diffraction pattern misidentified as different protein.",{"type":9,"tag":40,"props":1050,"children":1051},{},[],{"type":9,"tag":450,"props":1053,"children":1055},{"id":1054},"_2️⃣-honest-errors",[1056],{"type":14,"value":1057},"2️⃣ Honest errors",{"type":9,"tag":10,"props":1059,"children":1060},{},[1061],{"type":14,"value":1062},"Examples:",{"type":9,"tag":73,"props":1064,"children":1065},{},[1066,1071,1076],{"type":9,"tag":77,"props":1067,"children":1068},{},[1069],{"type":14,"value":1070},"Chain traced backwards",{"type":9,"tag":77,"props":1072,"children":1073},{},[1074],{"type":14,"value":1075},"Secondary structure misinterpreted",{"type":9,"tag":77,"props":1077,"children":1078},{},[1079],{"type":14,"value":1080},"Over-interpretation of low-resolution maps",{"type":9,"tag":10,"props":1082,"children":1083},{},[1084],{"type":14,"value":1085},"But:",{"type":9,"tag":10,"props":1087,"children":1088},{},[1089],{"type":14,"value":1090},"👉 Community validation usually corrects mistakes.",{"type":9,"tag":40,"props":1092,"children":1093},{},[],{"type":9,"tag":450,"props":1095,"children":1097},{"id":1096},"_3️⃣-over-interpretation",[1098],{"type":14,"value":1099},"3️⃣ Over-interpretation",{"type":9,"tag":10,"props":1101,"children":1102},{},[1103],{"type":14,"value":1104},"Typical cases:",{"type":9,"tag":73,"props":1106,"children":1107},{},[1108,1113,1118,1123],{"type":9,"tag":77,"props":1109,"children":1110},{},[1111],{"type":14,"value":1112},"Too many water molecules at low resolution",{"type":9,"tag":77,"props":1114,"children":1115},{},[1116],{"type":14,"value":1117},"Incorrect metal assignment",{"type":9,"tag":77,"props":1119,"children":1120},{},[1121],{"type":14,"value":1122},"Hydrogen atoms modeled without evidence",{"type":9,"tag":77,"props":1124,"children":1125},{},[1126],{"type":14,"value":1127},"Catalytic mechanisms inferred beyond data support",{"type":9,"tag":10,"props":1129,"children":1130},{},[1131],{"type":14,"value":1132},"Example insight:",{"type":9,"tag":73,"props":1134,"children":1135},{},[1136],{"type":9,"tag":77,"props":1137,"children":1138},{},[1139],{"type":14,"value":1140},"Magnesium vs calcium assignment must match coordination distances.",{"type":9,"tag":40,"props":1142,"children":1143},{},[],{"type":9,"tag":44,"props":1145,"children":1147},{"id":1146},"biological-interpretation-caveat",[1148],{"type":14,"value":1149},"🧠 Biological Interpretation Caveat",{"type":9,"tag":10,"props":1151,"children":1152},{},[1153,1154,1159],{"type":14,"value":392},{"type":9,"tag":17,"props":1155,"children":1156},{},[1157],{"type":14,"value":1158},"perfect crystal structure",{"type":14,"value":1160}," may represent:",{"type":9,"tag":73,"props":1162,"children":1163},{},[1164,1169,1174],{"type":9,"tag":77,"props":1165,"children":1166},{},[1167],{"type":14,"value":1168},"Inactive state",{"type":9,"tag":77,"props":1170,"children":1171},{},[1172],{"type":14,"value":1173},"Artifact of crystallization",{"type":9,"tag":77,"props":1175,"children":1176},{},[1177],{"type":14,"value":1178},"Non-physiological conformation",{"type":9,"tag":10,"props":1180,"children":1181},{},[1182],{"type":14,"value":1183},"Thus:",{"type":9,"tag":25,"props":1185,"children":1186},{},[1187],{"type":9,"tag":10,"props":1188,"children":1189},{},[1190],{"type":14,"value":1191},"Structure ≠ mechanism automatically.",{"type":9,"tag":10,"props":1193,"children":1194},{},[1195],{"type":14,"value":1196},"Multiple structures + biochemical data are essential.",{"type":9,"tag":40,"props":1198,"children":1199},{},[],{"type":9,"tag":44,"props":1201,"children":1203},{"id":1202},"final-practical-checklist-from-the-papers-philosophy",[1204],{"type":14,"value":1205},"🧪 Final Practical Checklist (From the Paper’s Philosophy)",{"type":9,"tag":10,"props":1207,"children":1208},{},[1209],{"type":14,"value":1210},"When reading a structural paper:",{"type":9,"tag":10,"props":1212,"children":1213},{},[1214],{"type":14,"value":1215},"✅ Check resolution vs level of claimed detail\n✅ Inspect number of waters / metals\n✅ Look at R and Rfree\n✅ Examine Ramachandran statistics\n✅ Check B-factors and occupancies\n✅ Ensure conclusions match data quality\n✅ Apply biochemical common sense",{"type":9,"tag":40,"props":1217,"children":1218},{},[],{"type":9,"tag":44,"props":1220,"children":1222},{"id":1221},"big-take-home-message",[1223],{"type":14,"value":1224},"⭐ Big Take-Home Message",{"type":9,"tag":10,"props":1226,"children":1227},{},[1228,1230],{"type":14,"value":1229},"Protein crystallography is ",{"type":9,"tag":17,"props":1231,"children":1232},{},[1233],{"type":14,"value":1234},"powerful but interpretative.",{"type":9,"tag":73,"props":1236,"children":1237},{},[1238,1243,1253],{"type":9,"tag":77,"props":1239,"children":1240},{},[1241],{"type":14,"value":1242},"Most structures are reliable.",{"type":9,"tag":77,"props":1244,"children":1245},{},[1246,1248],{"type":14,"value":1247},"But ",{"type":9,"tag":17,"props":1249,"children":1250},{},[1251],{"type":14,"value":1252},"critical evaluation is necessary.",{"type":9,"tag":77,"props":1254,"children":1255},{},[1256],{"type":14,"value":1257},"Built-in validation metrics make crystallography uniquely self-correcting.",1775084302999]