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Crystal structure of thrombin mutant S195T bound with PPACK
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 6.5 293 0.1 M MES, pH 6.5, 15% PEG 6000 and 5% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.593 α = 90 b = 73.31 β = 113.43 c = 48.706 γ = 90
Symmetry Space Group P 1 21 1
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++ 2014-06-20 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 1.84 40 92 0.081 13.4 3.7 24760 22779 -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 1.84 1.88 86.8 0.518 1.8 3.1 1072
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 1.84 40 -1 -1 23608 21578 1157 91.4 0.16796 0.16609 0.1762 0.20224 0.2111 RANDOM 40.172
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] -1.08 0.21 -1.31 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.972 r_dihedral_angle_3_deg 13.343 r_dihedral_angle_4_deg 13.068 r_dihedral_angle_1_deg 7.91 r_long_range_B_refined 7.696 r_long_range_B_other 7.641 r_scangle_other 5.592 r_scbond_it 3.649 r_scbond_other 3.649 r_mcangle_it 3.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.972 r_dihedral_angle_3_deg 13.343 r_dihedral_angle_4_deg 13.068 r_dihedral_angle_1_deg 7.91 r_long_range_B_refined 7.696 r_long_range_B_other 7.641 r_scangle_other 5.592 r_scbond_it 3.649 r_scbond_other 3.649 r_mcangle_it 3.425 r_mcangle_other 3.424 r_mcbond_it 2.428 r_mcbond_other 2.428 r_angle_refined_deg 1.326 r_angle_other_deg 0.836 r_chiral_restr 0.15 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2352 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 69
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling