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Structure of VD20_5A4 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F9W PDB entries 5F9W, 5DD5, 2BX5 experimental model PDB 5DD5 PDB entries 5F9W, 5DD5, 2BX5 experimental model PDB 2BX5 PDB entries 5F9W, 5DD5, 2BX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% PEG3000, 0.2 M sodium chloride, 0.1 M Tris, pH 7, 0.01 M praseodymium(III) acetate hydrate, cryoprotectant: 26% glycerol
Crystal Properties Matthews coefficient Solvent content 2.72 54.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.207 α = 90 b = 108.733 β = 105.775 c = 55.418 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.99 84.31 98.3 0.096 0.117 0.065 7.9 3 67170 37.9199020356
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.061 98.55 1.198 0.212 1.42 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entries 5F9W, 5DD5, 2BX5 1.99002311102 84.3040636766 1.33534688718 67147 3282 98.1107539451 0.200763057575 0.198942080158 0.2021 0.236317856463 0.2371 47.2163183524
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.1852560536 f_angle_d 0.968296625347 f_chiral_restr 0.0356851015842 f_bond_d 0.00528048744592 f_plane_restr 0.00425789408979
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6568 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling Coot model building PHASER phasing