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Crystal Structure of Proteinase K from Engyodontium albuminhibited by METHOXYSUCCINYL-ALA-ALA-PRO-PHE-CHLOROMETHYL KETONE at 1.15 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 Ammonium Sulfate , Tris HCL, calcium chloride
Crystal Properties Matthews coefficient Solvent content 1.97 37.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.85 α = 90 b = 67.85 β = 90 c = 102.51 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 DECTRIS PILATUS 6M 2014-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979200 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.15 56.6 97.2 0.067 0.07 18.82 12.2 82922 -3 16.018
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 1.15 1.18 74.4 0.591 0.63 3.26
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 FOURIER SYNTHESIS THROUGHOUT 3PRK 1.15 56.58 74629 8293 97.17 0.1124 0.1099 0.11 0.1345 0.1346 RANDOM 14.417
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] -0.1 -0.1 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.28 r_sphericity_free 25.404 r_dihedral_angle_4_deg 18.509 r_dihedral_angle_3_deg 11.252 r_dihedral_angle_1_deg 9.525 r_sphericity_bonded 8.843 r_rigid_bond_restr 4.257 r_angle_refined_deg 1.766 r_mcangle_it 1.376 r_mcbond_other 1.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.28 r_sphericity_free 25.404 r_dihedral_angle_4_deg 18.509 r_dihedral_angle_3_deg 11.252 r_dihedral_angle_1_deg 9.525 r_sphericity_bonded 8.843 r_rigid_bond_restr 4.257 r_angle_refined_deg 1.766 r_mcangle_it 1.376 r_mcbond_other 1.323 r_mcbond_it 1.322 r_angle_other_deg 0.9 r_chiral_restr 0.118 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2066 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 2
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing