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Complex of recombinant human thrombin with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OYT PDB ENTRY 1OYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 PH 7.40
Crystal Properties Matthews coefficient Solvent content 2.76 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.29 α = 90 b = 71.84 β = 100.56 c = 73.06 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 MARRESEARCH OSMIC MIRRORS 2004-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 1.79 20 91.4 0.04 22.9 4.54 31281 -3
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 1.79 1.9 86.6 0.25 5.4 4.13
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1OYT 1.79 71.8 29702 1582 91.5 0.162 0.16 0.16 0.198 0.1984 RANDOM 21.94
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] -0.8 -0.44 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.102 r_dihedral_angle_4_deg 12.718 r_dihedral_angle_3_deg 11.608 r_dihedral_angle_1_deg 6.117 r_scangle_it 2.498 r_scbond_it 1.607 r_angle_refined_deg 1.359 r_mcangle_it 1.035 r_mcbond_it 0.59 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.102 r_dihedral_angle_4_deg 12.718 r_dihedral_angle_3_deg 11.608 r_dihedral_angle_1_deg 6.117 r_scangle_it 2.498 r_scbond_it 1.607 r_angle_refined_deg 1.359 r_mcangle_it 1.035 r_mcbond_it 0.59 r_nbtor_refined 0.307 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.175 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 2301 Nucleic Acid Atoms Solvent Atoms 494 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling