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The catalytic domain of human plasma kallikrein with peptide inhibitor 070
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 298 PEG 3350, TRIS-HCL, (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.037 α = 90 b = 91.037 β = 90 c = 57.48 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 ADSC QUANTUM 315r 2014-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.77 50 98.9 0.117 0.985 17.34 7.4 26165
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.83 100 0.443 0.949 11.49 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.77 32.53 24885 1254 98.68 0.18514 0.18395 0.20992 0.2401 RANDOM 23.489
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] -0.08 -0.04 -0.08 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.489 r_long_range_B_refined 6.664 r_long_range_B_other 6.638 r_dihedral_angle_1_deg 6.535 r_dihedral_angle_2_deg 5.91 r_scangle_other 5.72 r_scbond_it 3.834 r_scbond_other 3.832 r_mcangle_it 3.356 r_mcangle_other 3.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.489 r_long_range_B_refined 6.664 r_long_range_B_other 6.638 r_dihedral_angle_1_deg 6.535 r_dihedral_angle_2_deg 5.91 r_scangle_other 5.72 r_scbond_it 3.834 r_scbond_other 3.832 r_mcangle_it 3.356 r_mcangle_other 3.355 r_mcbond_it 2.426 r_mcbond_other 2.39 r_angle_refined_deg 1.848 r_angle_other_deg 0.635 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1952 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing