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Crystal Structure of Thrombin in complex with compound42a
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 2.53 51.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.26 α = 90 b = 71.3 β = 100.43 c = 72.45 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 345 mm plate 2011-09-16 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 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 1.939 71.253 95.4 0.055 0.067 0.038 13 2.7 25381 25381
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 1.939 2.03 85.4 0.199 0.199 0.246 0.142 3.9 2.5
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 1.94 71.25 24062 1295 96.89 0.1644 0.1621 0.1755 0.206 0.2185 RANDOM 28.009
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] -0.28 -0.51 0.08 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.969 r_dihedral_angle_4_deg 16.434 r_dihedral_angle_3_deg 14.212 r_dihedral_angle_1_deg 6.562 r_angle_refined_deg 2.011 r_angle_other_deg 1.05 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.969 r_dihedral_angle_4_deg 16.434 r_dihedral_angle_3_deg 14.212 r_dihedral_angle_1_deg 6.562 r_angle_refined_deg 2.011 r_angle_other_deg 1.05 r_chiral_restr 0.117 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2348 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 47
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction