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High resolution crystal structure of proteinase K with thiourea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 273 1.28M ammonium sulfate, 0.1M Tris-HCl, pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.03 39.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.842 α = 90 b = 67.842 β = 90 c = 102.377 γ = 90
Symmetry Space Group P 43 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 PIXEL Bruker PHOTON II 2019-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.45 19.79 99.9 0.065 0.092 0.99 12.4 1.9 43099 14.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.45 99.5 0.557 0.787 1.9 1.8
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 (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 1PEK 1.45 19.79 40867 2162 99.9 0.1688 0.1682 0.1686 0.1795 0.1792 RANDOM 6.304
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.722 r_dihedral_angle_4_deg 14.647 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 6.718 r_angle_other_deg 2.479 r_angle_refined_deg 1.747 r_mcangle_it 0.885 r_mcbond_it 0.607 r_mcbond_other 0.57 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.722 r_dihedral_angle_4_deg 14.647 r_dihedral_angle_3_deg 12.863 r_dihedral_angle_1_deg 6.718 r_angle_other_deg 2.479 r_angle_refined_deg 1.747 r_mcangle_it 0.885 r_mcbond_it 0.607 r_mcbond_other 0.57 r_chiral_restr 0.082 r_bond_other_d 0.038 r_gen_planes_other 0.017 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2025 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Aimless data scaling Coot model building