☰ Navigation Tabs
The Crystal Structure of Bovine Thrombin in complex with Hirudin (C22U/C39U) at 2.7 Angstroms Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7A0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 297 38% PEG 4000, 0.1 M sodium phosphate (pH= 4.7), 0.3 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.46 49.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.069 α = 90 b = 101.498 β = 90 c = 142.075 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.9778 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.7 47.79 100 0.287 0.287 0.299 0.082 0.992 8.9 13.1 11928
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) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.83 1.8 1.8 1.873 0.514 0.592 1.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7A0D 2.7 47.79 11902 586 99.933 0.196 0.1936 0.1945 0.2532 0.2516 45.168
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] -0.848 0.639 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.42 r_dihedral_angle_4_deg 20.966 r_dihedral_angle_3_deg 17.975 r_lrange_it 10.929 r_dihedral_angle_1_deg 10.113 r_scangle_it 6.841 r_mcangle_it 5.638 r_scbond_it 4.378 r_mcbond_it 3.456 r_angle_refined_deg 1.744
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.42 r_dihedral_angle_4_deg 20.966 r_dihedral_angle_3_deg 17.975 r_lrange_it 10.929 r_dihedral_angle_1_deg 10.113 r_scangle_it 6.841 r_mcangle_it 5.638 r_scbond_it 4.378 r_mcbond_it 3.456 r_angle_refined_deg 1.744 r_nbtor_refined 0.314 r_symmetry_xyhbond_nbd_refined 0.286 r_ext_dist_refined_d 0.278 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.208 r_xyhbond_nbd_refined 0.147 r_metal_ion_refined 0.141 r_chiral_restr 0.126 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2848 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 15
Software Software Software Name Purpose XDS data processing Aimless data reduction Aimless data scaling PHASER phasing Coot model building REFMAC refinement