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Complex of Recombinant Human Thrombin with a Designed Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CF8 PDB ENTRY 2CF8.PDB
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 = 70.64 α = 90 b = 71.41 β = 100.35 c = 72.52 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 2005-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.3 50 96.4 0.07 14.2 4.67 83900
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 1.3 1.37 100 0.37 5.1 4.14
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 2CF8.PDB 1.3 71.43 79708 4196 96.5 0.185 0.184 0.1859 0.204 0.207 RANDOM 20.19
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] 0.04 -0.84 -0.83 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.331 r_dihedral_angle_4_deg 14.312 r_dihedral_angle_3_deg 12.191 r_dihedral_angle_1_deg 5.862 r_scangle_it 2.671 r_scbond_it 1.858 r_angle_refined_deg 1.597 r_mcangle_it 1.363 r_angle_other_deg 0.826 r_mcbond_it 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.331 r_dihedral_angle_4_deg 14.312 r_dihedral_angle_3_deg 12.191 r_dihedral_angle_1_deg 5.862 r_scangle_it 2.671 r_scbond_it 1.858 r_angle_refined_deg 1.597 r_mcangle_it 1.363 r_angle_other_deg 0.826 r_mcbond_it 0.812 r_symmetry_vdw_other 0.304 r_nbd_refined 0.197 r_nbd_other 0.187 r_nbtor_refined 0.184 r_symmetry_hbond_refined 0.16 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.1 r_nbtor_other 0.091 r_symmetry_vdw_refined 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 2301 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling