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Protein Data Bank Contents Guide: Atomic Coordinate Entry Format

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Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.20 Document Published by the wwPDB This format complies with the PDB Exchange Dictionary (PDBx) http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/Index/index.html. ©2008 wwPDB PDB File Format v. 3.2 Page i Table of Contents 1. Introduction................................................................................................................................... 1 Basic Notions of the Format Description ............................................................................................3 Record Format....................................................................................................................................5 Types of Records................................................................................................................................6 PDB Format Change Policy................................................................................................................9 Order of Records ..............................................................................................................................10 Sections of an Entry..........................................................................................................................12 Field Formats and Data Types .........................................................................................................14 2. Title Section................................................................................................................................ 16 HEADER...........................................................................................................................................16 OBSLTE............................................................................................................................................19 TITLE................................................................................................................................................21 SPLIT (added) ..................................................................................................................................22 CAVEAT ...........................................................................................................................................23 COMPND (updated) .........................................................................................................................24 SOURCE (updated) ..........................................................................................................................26 KEYWDS ..........................................................................................................................................31 EXPDTA (updated) ...........................................................................................................................33 NUMMDL (added).............................................................................................................................35 MDLTYP (added)..............................................................................................................................36 AUTHOR...........................................................................................................................................38 REVDAT (updated)...........................................................................................................................40 SPRSDE ...........................................................................................................................................42 JRNL (updated) ................................................................................................................................44 REMARK ..........................................................................................................................................52 REMARKs 0-5......................................................................................................................... 52 REMARK 0 (added), Re-refinement notice ...............................................................................52 REMARK 1 (updated), Related publications .............................................................................54 REMARK 2 (updated), Resolution.............................................................................................60 REMARK 3 (updated), Final refinement information .................................................................62 Refinement using X-PLOR ........................................................................................................63 Refinement using CNS..............................................................................................................65 Refinement using CNX..............................................................................................................67 Refinement using REFMAC ......................................................................................................69 Refinement using NUCLSQ ......................................................................................................77 Refinement using SHELXL........................................................................................................81 Refinement using TNT/BUSTER...............................................................................................83 Refinement using PHENIX ........................................................................................................86 Refinement using BUSTER-TNT...............................................................................................94 Example for Solution Scattering ................................................................................................99 Non-diffraction studies...............................................................................................................99 REMARK 4 (updated), Format ................................................................................................100 REMARK 5 (updated), Obsolete Statement............................................................................100 PDB File Format v. 3.2 Page ii REMARKs 6 - 99................................................................................................................... 101 REMARK 100 (updated), Deposition or Processing Site ...................................................... 101 REMARKs 200-265, Experimental Details............................................................................ 102 REMARK 200 (updated), X-ray Diffraction Experimental Details............................................102 REMARK 205, Fiber Diffraction, Fiber Sample Experiment Details ........................................105 REMARKs 210 and 215/217, NMR Experiment Details..........................................................105 REMARK 230, Neutron Diffraction Experiment Details...........................................................107 REMARK 240 (updated), Electron Crystallography Experiment Details .................................110 REMARK 245 (updated), Electron Microscopy Experiment Details ........................................112 REMARK 247, Electron Microscopy details ............................................................................114 REMARK 250, Other Type of Experiment Details...................................................................114 REMARK 265, Solution Scattering Experiment Details...........................................................115 REMARKs 280-290, Crystallographic Details ....................................................................... 117 REMARK 280, Crystal.............................................................................................................117 REMARK 285, CRYST1..........................................................................................................117 REMARK 290, Crystallographic Symmetry .............................................................................118 REMARK 300 (updated), Biomolecule ....................................................................................119 REMARK 350 (updated), Generating the Biomolecule ...........................................................121 Example – When software predicts multiple quaternary assemblies ......................................123 REMARK 375 (updated), Special Position ..............................................................................125 REMARK 400, Compound ......................................................................................................125 REMARK 450, Source.............................................................................................................126 REMARK 465 (updated), Missing residues.............................................................................126 REMARK 470 (updated), Missing Atom(s)..............................................................................127 REMARK 475 (added), Residues modeled with zero occupancy ...........................................128 REMARK 480 (added), Polymer atoms modeled with zero occupancy ..................................129 REMARK 500 (updated), Geometry and Stereochemistry......................................................130 REMARK 525 (updated), Distant Solvent Atoms ....................................................................136 REMARK 600, Heterogen .......................................................................................................136
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