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Structure of thrombin mutant S195a bound to the active site inhibitor argatroban
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 100mM Na acetate pH 4.6 and 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.229 α = 90 b = 77.229 β = 90 c = 94.875 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2012-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.4 40.42 98.9 0.107 13.9 6.3 21851 21611 -0.2 -0.2
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 2.4 2.44 91.5 0.362 2.8 3.1 990
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 1SHH 2.4 40.42 20733 20437 1105 98.57 0.17049 0.167 0.2074 0.23805 0.2523 RANDOM 55.751
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] 3.77 3.77 -7.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.848 r_dihedral_angle_3_deg 17.231 r_dihedral_angle_4_deg 14.425 r_dihedral_angle_1_deg 5.169 r_angle_refined_deg 0.994 r_scangle_it 0.636 r_scbond_it 0.401 r_mcangle_it 0.258 r_mcbond_it 0.141 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.848 r_dihedral_angle_3_deg 17.231 r_dihedral_angle_4_deg 14.425 r_dihedral_angle_1_deg 5.169 r_angle_refined_deg 0.994 r_scangle_it 0.636 r_scbond_it 0.401 r_mcangle_it 0.258 r_mcbond_it 0.141 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4637 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 72
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling