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Crystal Structure of Thrombin in complex with compound17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other inhouse
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 283 0.02 M phosphate buffer pH 7.5,
27% PEG 8000, 100 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.52 51.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.091 α = 90 b = 71.054 β = 100.51 c = 72.62 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 IMAGE PLATE MAR scanner 300 mm plate 2009-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.541870
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.7 20.43 82.6 0.047 0.047 0.056 0.029 17.9 3.4 31839 31839
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 31.5 0.265 0.025 0.03 0.016 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT inhouse 1.7 15 30248 1589 82.51 0.1802 0.1781 0.1798 0.2178 0.2196 RANDOM 26.847
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] 0.21 -0.27 -0.55 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.328 r_dihedral_angle_3_deg 13.406 r_dihedral_angle_4_deg 12.234 r_dihedral_angle_1_deg 6.793 r_angle_refined_deg 2.342 r_chiral_restr 0.106 r_bond_refined_d 0.012 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2348 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 48
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction