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Crystal structure of BbKI complexed with Human Kallikrein 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JOD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25% PEG3350, 0.2M NaCl
Crystal Properties Matthews coefficient Solvent content 3.5 64.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.296 α = 90 b = 92.296 β = 90 c = 119.547 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 PIXEL DECTRIS EIGER X 16M 2019-12-16 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 Sym I (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 2.6 50 98.6 0.058 37 9.8 17558
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 0.697 1.35
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 7JOD 2.6 43.09 14233 746 84.27 0.1884 0.1864 0.1917 0.2255 0.2221 RANDOM 39.799
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] -0.63 -0.32 -0.63 2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.238 r_dihedral_angle_4_deg 23.033 r_dihedral_angle_3_deg 21.56 r_dihedral_angle_1_deg 9.99 r_angle_refined_deg 2.143 r_angle_other_deg 1.442 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.238 r_dihedral_angle_4_deg 23.033 r_dihedral_angle_3_deg 21.56 r_dihedral_angle_1_deg 9.99 r_angle_refined_deg 2.143 r_angle_other_deg 1.442 r_chiral_restr 0.087 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2947 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing