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Crystal structure of BbKI, a disulfide-free plasma kallikrein inhibitor at 1.4 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GO2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 rBbKI in 0.05 M Tris/HCl, pH 8.0, and 0.15 M NaCl was concentrated to 6.3 mg/ml and crystallized using the conditions 8% PEG 4000, 0.1 M sodium acetate, pH 4.6. Cryoprotectant solution - mother liquor with extra 25% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.42 49.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.736 α = 90 b = 59.462 β = 90 c = 64.011 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2013-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.4 50 96.1 0.048 0.048 0.054 0.024 10.2 5 34445 -3 16.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 93.3 0.628 0.704 0.311 0.752 1.9 4.8 1631
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 2GO2 1.4 43.57 32686 1726 96.06 0.1247 0.1226 0.1218 0.1665 0.1661 RANDOM 23.091
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] -0.44 0.11 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.022 r_sphericity_free 29.752 r_dihedral_angle_4_deg 23.965 r_sphericity_bonded 16.485 r_dihedral_angle_3_deg 11.197 r_dihedral_angle_1_deg 7.645 r_mcangle_it 3.656 r_mcbond_it 2.943 r_mcbond_other 2.941 r_rigid_bond_restr 2.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.022 r_sphericity_free 29.752 r_dihedral_angle_4_deg 23.965 r_sphericity_bonded 16.485 r_dihedral_angle_3_deg 11.197 r_dihedral_angle_1_deg 7.645 r_mcangle_it 3.656 r_mcbond_it 2.943 r_mcbond_other 2.941 r_rigid_bond_restr 2.817 r_angle_other_deg 1.86 r_angle_refined_deg 1.779 r_chiral_restr 0.169 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1248 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms
Software Software Software Name Purpose SERGUI data collection HKL-3000 data reduction HKL-3000 data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction