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The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ANY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 28% PEG 3350, 0.1M TRIS-HCL PH8.5, 20MM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.279 α = 90 b = 90.279 β = 90 c = 57.623 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2014-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.5 78.18 99.4 14.2 5.7 42363
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2ANY 1.5 50 40208 2132 99.11 0.18116 0.17933 0.1854 0.21747 0.2256 RANDOM 19.358
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 0.01 0.02 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.865 r_sphericity_free 19.877 r_dihedral_angle_4_deg 13.746 r_dihedral_angle_3_deg 12.767 r_dihedral_angle_1_deg 6.031 r_sphericity_bonded 5.125 r_long_range_B_refined 2.441 r_long_range_B_other 2.441 r_scangle_other 1.89 r_scbond_it 1.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.865 r_sphericity_free 19.877 r_dihedral_angle_4_deg 13.746 r_dihedral_angle_3_deg 12.767 r_dihedral_angle_1_deg 6.031 r_sphericity_bonded 5.125 r_long_range_B_refined 2.441 r_long_range_B_other 2.441 r_scangle_other 1.89 r_scbond_it 1.881 r_scbond_other 1.88 r_rigid_bond_restr 1.832 r_mcangle_other 1.566 r_mcangle_it 1.563 r_angle_refined_deg 1.413 r_mcbond_it 1.35 r_mcbond_other 1.335 r_angle_other_deg 0.94 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1966 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling