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Human VKOR with Brodifacoum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3P PDB entry 2B3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.5 295 32% PEG400, 0.1 M ammonium acetate, 1% 1,2,3-heptanetriol, 0.1 M MES, pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.03 59.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.576 α = 93.417 b = 82.593 β = 97.481 c = 78.61 γ = 104.685
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 PILATUS 6M-F 2017-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 50 90.7 0.068 0.088 0.055 9.2 2.3 63563 23.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 91.7 0.415 0.541 0.343 0.747 2.2
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 entry 2B3P 1.99 30.47 1.97 63544 3223 90.25 0.1956 0.1946 0.1954 0.215 0.2151 29.69
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 18.3477 f_angle_d 0.7935 f_chiral_restr 0.0496 f_plane_restr 0.0049 f_bond_d 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6123 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing