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Crystal structure of the complex of proteinase K with a specific lactoferrin peptide Val-Leu-Leu-His at 1.93 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 7.5 298 sodium nitrate, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.313 α = 90 b = 68.313 β = 90 c = 108.407 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 291 IMAGE PLATE MAR scanner 345 mm plate mirror 2006-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.93 57.74 98.6 19884 19884
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.93 1.96 99.2
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 3PRK 1.93 57.74 19884 18805 1012 99.19 0.16 0.1536 0.15182 0.1871 RANDOM 13.263
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] -0.16 -0.16 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.529 r_dihedral_angle_1_deg 3.848 r_scangle_it 3.315 r_scbond_it 1.931 r_angle_refined_deg 1.318 r_mcangle_it 0.996 r_mcbond_it 0.496 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.161
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.529 r_dihedral_angle_1_deg 3.848 r_scangle_it 3.315 r_scbond_it 1.931 r_angle_refined_deg 1.318 r_mcangle_it 0.996 r_mcbond_it 0.496 r_symmetry_vdw_refined 0.232 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.161 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.085 r_metal_ion_refined 0.029 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2064 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing