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Crystal structure of proteinase K inhibited by a lactoferrin octapeptide Gly-Asp-Glu-Gln-Gly-Glu-Asn-Lys at 2.15 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, HANGING DROP 4.6 298 0.2M Ammonium acetate, 0.1M Sodium acetate hydrate, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 41.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.366 α = 90 b = 68.366 β = 90 c = 108.079 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 2006-05-05 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 2.15 20 99.1 0.075 7.1 14558 14558 20.968
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) 2.15 2.23 100 0.249 2.1
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 1P7V 2.15 20 14493 13764 729 99.77 0.17003 0.17242 0.17066 0.2024 RANDOM 18.925
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] -0.07 -0.07 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.622 r_dihedral_angle_4_deg 19.313 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 5.574 r_scangle_it 2.226 r_scbond_it 1.468 r_angle_refined_deg 1.125 r_mcangle_it 0.854 r_mcbond_it 0.506 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.622 r_dihedral_angle_4_deg 19.313 r_dihedral_angle_3_deg 12.967 r_dihedral_angle_1_deg 5.574 r_scangle_it 2.226 r_scbond_it 1.468 r_angle_refined_deg 1.125 r_mcangle_it 0.854 r_mcbond_it 0.506 r_nbtor_refined 0.295 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.149 r_symmetry_vdw_refined 0.132 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.077 r_metal_ion_refined 0.022 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2170 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing