☰ Navigation Tabs
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 = 71.07 α = 90 b = 71.51 β = 100.25 c = 72.4 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 2005-10-28 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 20 98.2 0.04 17.8 3.58 85919 -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 1.3 1.37 95.9 0.3 4.2 3.08
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1OYT 1.3 71.25 81614 4308 98.2 0.181 0.18 0.199 0.2907 RANDOM 24.05
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] -0.01 -0.71 -0.13 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.054 r_dihedral_angle_4_deg 13.204 r_dihedral_angle_3_deg 11.166 r_dihedral_angle_1_deg 6.066 r_scangle_it 2.701 r_scbond_it 1.957 r_angle_refined_deg 1.603 r_mcangle_it 1.332 r_angle_other_deg 0.832 r_mcbond_it 0.797
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.054 r_dihedral_angle_4_deg 13.204 r_dihedral_angle_3_deg 11.166 r_dihedral_angle_1_deg 6.066 r_scangle_it 2.701 r_scbond_it 1.957 r_angle_refined_deg 1.603 r_mcangle_it 1.332 r_angle_other_deg 0.832 r_mcbond_it 0.797 r_symmetry_vdw_other 0.32 r_nbd_refined 0.196 r_nbd_other 0.187 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.115 r_nbtor_other 0.082 r_symmetry_vdw_refined 0.041 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 2301 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling