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Crystal structure of proteinase K complex with a synthetic peptide KLKLLVVIRLK at 1.69 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 50mM TRIS, 10mM CaCl2, 1M NaNO3, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.312 α = 90 b = 68.312 β = 90 c = 108.381 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 298 IMAGE PLATE MARRESEARCH MIRROR 2006-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5414
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 1.69 20 99.6 0.068 9.5 29433 29433 18.821
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) 1.69 1.75 100 0.318 2.3
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1P7V 1.69 20 28397 28397 943 99.69 0.15983 0.1592 0.17944 RANDOM 20.99
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] -0.15 -0.15 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.932 r_dihedral_angle_4_deg 21.338 r_dihedral_angle_3_deg 14.117 r_dihedral_angle_1_deg 5.801 r_scangle_it 3.529 r_scbond_it 2.363 r_angle_refined_deg 1.244 r_mcangle_it 1.23 r_mcbond_it 0.761 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.932 r_dihedral_angle_4_deg 21.338 r_dihedral_angle_3_deg 14.117 r_dihedral_angle_1_deg 5.801 r_scangle_it 3.529 r_scbond_it 2.363 r_angle_refined_deg 1.244 r_mcangle_it 1.23 r_mcbond_it 0.761 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.086 r_symmetry_hbond_refined 0.065 r_metal_ion_refined 0.038 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2230 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling AMoRE phasing