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Crystal Structure of Thrombin in complex with compound51
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 2.42 49.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.166 α = 90 b = 70.342 β = 100.28 c = 71.372 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 CCD Nonius Kappa CCD MIRRORS 2012-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.59 70.23 89.2 0.06 12.95 2.84 130734 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.61 89 0.279 1.96
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 70.22 31333 1618 88.88 0.2052 0.203 0.2117 0.2473 0.2505 RANDOM 18.885
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] 0.57 -0.38 -0.45 -0.05
RMS Deviations Key Refinement Restraint Deviation TORSION ANGLES, PERIOD 2 (DEGREES) 33.059 TORSION ANGLES, PERIOD 3 (DEGREES) 14.353 TORSION ANGLES, PERIOD 4 (DEGREES) 12.948 TORSION ANGLES, PERIOD 1 (DEGREES) 6.86 BOND ANGLES REFINED (DEGREES) 2.212 BOND ANGLES OTHERS (DEGREES) 0.915 CHIRAL-CENTER RESTRAINTS (A**3) 0.121 BOND LENGTHS REFINED (A) 0.023 GENERAL PLANES REFINED (A) 0.012 BOND LENGTHS OTHERS (A) 0.002
RMS Deviations Key Refinement Restraint Deviation TORSION ANGLES, PERIOD 2 (DEGREES) 33.059 TORSION ANGLES, PERIOD 3 (DEGREES) 14.353 TORSION ANGLES, PERIOD 4 (DEGREES) 12.948 TORSION ANGLES, PERIOD 1 (DEGREES) 6.86 BOND ANGLES REFINED (DEGREES) 2.212 BOND ANGLES OTHERS (DEGREES) 0.915 CHIRAL-CENTER RESTRAINTS (A**3) 0.121 BOND LENGTHS REFINED (A) 0.023 GENERAL PLANES REFINED (A) 0.012 BOND LENGTHS OTHERS (A) 0.002 GENERAL PLANES OTHERS (A) 0.001 NON-BONDED CONTACTS REFINED (A) NON-BONDED CONTACTS OTHERS (A) NON-BONDED TORSION REFINED (A) NON-BONDED TORSION OTHERS (A) H-BOND (X...Y) REFINED (A) SYMMETRY VDW REFINED (A) SYMMETRY VDW OTHERS (A) SYMMETRY H-BOND REFINED (A)
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2342 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 14
Software Software Software Name Purpose SAINT data reduction XPREP data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction