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The Crystal Structure of Bovine Thrombin in complex with Hirudin (C6U/C14U) at 1.9 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), and 0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.6 52.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.099 α = 90 b = 101.995 β = 90 c = 144.044 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 EIGER2 XE 16M 2020-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
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 1.9 72.02 98.05 0.206 0.206 0.216 0.062 0.992 5 10.6 33481
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 1.9 1.93 1.848 1.848 2.148 1.061 0.873 0.2
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 1.9 72.02 33424 1572 97.894 0.216 0.2139 0.2144 0.2629 0.2635 40.955
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] 0.548 -0.38 -0.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 19.236 r_dihedral_angle_3_deg 16.33 r_lrange_it 8.384 r_dihedral_angle_1_deg 7.362 r_scangle_it 5.734 r_mcangle_it 4.208 r_scbond_it 3.906 r_mcbond_it 2.78 r_angle_refined_deg 1.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.672 r_dihedral_angle_4_deg 19.236 r_dihedral_angle_3_deg 16.33 r_lrange_it 8.384 r_dihedral_angle_1_deg 7.362 r_scangle_it 5.734 r_mcangle_it 4.208 r_scbond_it 3.906 r_mcbond_it 2.78 r_angle_refined_deg 1.453 r_nbtor_refined 0.314 r_symmetry_nbd_refined 0.274 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.108 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2852 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 15
Software Software Software Name Purpose xia2 data processing xia2 data reduction xia2 data scaling PHASER phasing Coot model building REFMAC refinement