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Active site thrombin inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QJ1 PDB ENTRY 1QJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.3 PH 7.30
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.503 α = 90 b = 71.512 β = 100.46 c = 72.205 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 RIGAKU CCD CONFOCAL MULTILAYER 2002-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2 71 97.7 0.07 2.7 1.9 23016
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 2.02 2.07 99.1 0.32 3 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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QJ1 2.02 49.78 21428 1135 98 0.161 0.158 0.231 RANDOM 18.37
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] 0.65 -0.54 -0.55 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.917 r_dihedral_angle_4_deg 16.74 r_dihedral_angle_3_deg 13.724 r_dihedral_angle_1_deg 6.458 r_scangle_it 4.897 r_scbond_it 3.699 r_mcangle_it 3.561 r_mcbond_it 3.235 r_angle_refined_deg 1.458 r_angle_other_deg 0.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.917 r_dihedral_angle_4_deg 16.74 r_dihedral_angle_3_deg 13.724 r_dihedral_angle_1_deg 6.458 r_scangle_it 4.897 r_scbond_it 3.699 r_mcangle_it 3.561 r_mcbond_it 3.235 r_angle_refined_deg 1.458 r_angle_other_deg 0.808 r_symmetry_vdw_other 0.307 r_nbd_refined 0.223 r_symmetry_hbond_refined 0.204 r_nbd_other 0.188 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.089 r_nbtor_other 0.083 r_symmetry_vdw_refined 0.067 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2356 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling IN-HOUSE phasing