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Structure of thrombin bound to BAY 3389934
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other In-house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.02M phosphate buffer at pH 7.5, 27% PEG 8000 and 100mM sodium chloride. Thrombin seeds were added to the final drop
Crystal Properties Matthews coefficient Solvent content 2.57 52.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.766 α = 90 b = 71.817 β = 99.97 c = 72.026 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 PILATUS 200K 2021-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 1.8 23.65 99.7 0.052 0.056 0.999 25.92 5.11 32428
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 1.8 1.9 0.245 0.295 0.948 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 23.65 1.35 32414 1605 99.72 0.1772 0.1759 0.1814 0.2003 0.2057 24.11
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 17.237 f_angle_d 1.9943 f_chiral_restr 0.1138 f_bond_d 0.0197 f_plane_restr 0.0146
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2348 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement PHENIX refinement CrysalisPro data reduction SHELXPREP data scaling PHASER phasing