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Crystal structure of thrombin mutant S195T (free form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SHH PDB ID 1SHH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 0.2 M K formate and 21% PEG3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.415 α = 90 b = 91.114 β = 90 c = 50.553 γ = 90
Symmetry Space Group P 21 21 2
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++ 2014-04-11 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 1.7 40 99.8 0.086 20.3 7.8 31959 31895 -1 -1
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 1.7 1.7 98.8 0.561 2.9 6 1540
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 PDB ID 1SHH 1.7 40 -1 -1 30326 30132 1605 99.36 0.15866 0.15612 0.1663 0.2071 0.2163 RANDOM 35.353
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] -1.1 2.19 -1.09
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.233 r_sphericity_bonded 16.197 r_long_range_B_refined 5.1 r_long_range_B_other 4.678 r_scangle_other 3.672 r_mcangle_it 3.232 r_mcangle_other 3.232 r_scbond_it 3.07 r_scbond_other 3.07 r_mcbond_it 2.594
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.233 r_sphericity_bonded 16.197 r_long_range_B_refined 5.1 r_long_range_B_other 4.678 r_scangle_other 3.672 r_mcangle_it 3.232 r_mcangle_other 3.232 r_scbond_it 3.07 r_scbond_other 3.07 r_mcbond_it 2.594 r_mcbond_other 2.557 r_rigid_bond_restr 2.05 r_angle_refined_deg 1.082 r_angle_other_deg 0.738 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2293 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 19
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling