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complex of human thrombin with XC-43
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2 M magnesium acetate, 9 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.32 62.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.35 α = 90 b = 136.32 β = 90 c = 193.95 γ = 90
Symmetry Space Group P 21 21 21
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 2020-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.15 44.24 99.9 0.085 0.089 0.999 18.27 11.189 163186 35.68
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 100 0.697 0.729 0.942 4.22 11.598
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 THROUGHOUT 1PPB 2.15 44.24 1.51 158863 8012 97.31 0.1659 0.1645 0.1659 0.1927 0.1949 43.0751
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14984 Nucleic Acid Atoms Solvent Atoms 1163 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction