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The Crystal Structure of Bovine Thrombin in complex with Hirudin (C16U/C28U) at 1.6 Angstroms Resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HRT
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), 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.52 51.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.672 α = 90 b = 102.374 β = 90 c = 142.735 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 2019-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9786 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.6 48.18 99.9 0.096 0.096 0.1 0.028 0.999 13.8 13 56998
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 1.6 1.63 98.3 2.37 2.37 2.47 0.693 0.421 1.1 12.5
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 1HRT 1.6 48.18 56953 2797 99.865 0.184 0.1828 0.1844 0.2154 0.2166 33.055
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] 0.401 -0.722 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.568 r_dihedral_angle_4_deg 20.721 r_dihedral_angle_3_deg 13.733 r_lrange_it 8.481 r_dihedral_angle_1_deg 7.014 r_scangle_it 6.803 r_scbond_it 4.586 r_mcangle_it 4.122 r_mcbond_it 2.904 r_angle_refined_deg 1.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.568 r_dihedral_angle_4_deg 20.721 r_dihedral_angle_3_deg 13.733 r_lrange_it 8.481 r_dihedral_angle_1_deg 7.014 r_scangle_it 6.803 r_scbond_it 4.586 r_mcangle_it 4.122 r_mcbond_it 2.904 r_angle_refined_deg 1.814 r_nbtor_refined 0.317 r_symmetry_nbd_refined 0.283 r_symmetry_xyhbond_nbd_refined 0.208 r_nbd_refined 0.207 r_chiral_restr 0.136 r_xyhbond_nbd_refined 0.133 r_metal_ion_refined 0.099 r_gen_planes_refined 0.011 r_bond_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2801 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 29
Software Software Software Name Purpose DIALS data processing Aimless data scaling Aimless data reduction PHENIX phasing Coot model building REFMAC refinement