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Crystal structure of the complex of Proteinase K with a designed heptapeptide inhibitor Pro-Ala-Pro-Phe-Ala-Ser-Ala at atomic resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IC6 PDB ENTRY 1IC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microgravity with APCF reactors 6.5 295 Tris HCl, CaCl2, NaNO3, pH 6.5, microgravity with APCF reactors, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.97 37.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.835 α = 90 b = 67.835 β = 90 c = 101.563 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 IMAGE PLATE MARRESEARCH mirrors 2000-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.91 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.02 20 99 0.063 24.4 15.8 119205 119205 -3 -3 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.02 1.06 95 0.234 5.58 11282
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IC6 1.02 20 119205 119205 1192 99.82 0.12917 0.1291 0.12904 0.14162 RANDOM 7.92
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
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 6.967 r_dihedral_angle_1_deg 6.716 r_scangle_it 3.736 r_scbond_it 2.486 r_sphericity_bonded 2.461 r_mcangle_it 1.704 r_angle_refined_deg 1.482 r_rigid_bond_restr 1.095 r_mcbond_it 1.066 r_angle_other_deg 0.919
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 6.967 r_dihedral_angle_1_deg 6.716 r_scangle_it 3.736 r_scbond_it 2.486 r_sphericity_bonded 2.461 r_mcangle_it 1.704 r_angle_refined_deg 1.482 r_rigid_bond_restr 1.095 r_mcbond_it 1.066 r_angle_other_deg 0.919 r_symmetry_vdw_refined 0.543 r_symmetry_vdw_other 0.412 r_symmetry_hbond_refined 0.409 r_nbd_other 0.276 r_nbd_refined 0.263 r_chiral_restr 0.218 r_xyhbond_nbd_refined 0.199 r_nbtor_other 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2077 Nucleic Acid Atoms Solvent Atoms 432 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing