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Structure of a complex formed between Proteinase K and a designed heptapeptide inhibitor Pro-Ala-Pro-Phe-Ala-Ala-Ala at atomic resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 37.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.72 α = 90 b = 67.72 β = 90 c = 101.62 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 2000-10-11 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 1.08 20 99.5 0.047 28 15.32 101462 101462 -3 -3 4.5
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) 1.08 1.12 99 0.234 5.61 11322
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1c6 1.08 20 101462 1015 99.65 0.11994 0.11974 0.13993 RANDOM 7.213
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] -0.02 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.295 r_scangle_it 2.998 r_sphericity_free 2.615 r_scbond_it 1.965 r_sphericity_bonded 1.851 r_angle_refined_deg 1.411 r_mcangle_it 1.336 r_angle_other_deg 1.017 r_rigid_bond_restr 0.882 r_mcbond_it 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.295 r_scangle_it 2.998 r_sphericity_free 2.615 r_scbond_it 1.965 r_sphericity_bonded 1.851 r_angle_refined_deg 1.411 r_mcangle_it 1.336 r_angle_other_deg 1.017 r_rigid_bond_restr 0.882 r_mcbond_it 0.814 r_symmetry_vdw_other 0.307 r_nbd_other 0.258 r_nbd_refined 0.243 r_symmetry_hbond_refined 0.23 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.132 r_nbtor_other 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4035 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing