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The crystal structure of human plasma kallikrein in complex with its peptide inhibitor pkalin-3
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 23% PEG 3350, 0.1M TRIS-HCL, PH 8.5, 20MM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.339 α = 90 b = 90.339 β = 90 c = 57.346 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 2014-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97 SSRF BL17U
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 1.55 50 100 26.2 5.5 38722
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 1.55 50 36754 1939 99.9 0.222 0.221 0.2112 0.243 0.2311 RANDOM 21.91
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] -0.09 -0.04 -0.09 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.654 r_dihedral_angle_3_deg 12.582 r_dihedral_angle_4_deg 8.545 r_dihedral_angle_1_deg 6.158 r_long_range_B_refined 4.801 r_long_range_B_other 4.256 r_mcangle_it 1.57 r_mcangle_other 1.569 r_scangle_other 1.349 r_angle_refined_deg 1.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.654 r_dihedral_angle_3_deg 12.582 r_dihedral_angle_4_deg 8.545 r_dihedral_angle_1_deg 6.158 r_long_range_B_refined 4.801 r_long_range_B_other 4.256 r_mcangle_it 1.57 r_mcangle_other 1.569 r_scangle_other 1.349 r_angle_refined_deg 1.185 r_mcbond_it 0.886 r_mcbond_other 0.886 r_scbond_it 0.877 r_scbond_other 0.821 r_angle_other_deg 0.742 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1955 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling