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Crystal Structure of Class A Beta-lactamase from Bacillus cereus in the Complex with the Beta-lactamase Inhibitor Clavulanate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QHY PDBID 3QHY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 0.2 M Magnesium chloride, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.728 α = 85.081 b = 43.643 β = 88.25 c = 72.404 γ = 86.677
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 PILATUS3 X 6M 2019-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97911 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 50 98.9 0.128 0.975 17 6 43737 29.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 97.2 0.581 0.852 1.92 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDBID 3QHY 1.85 37.13 1.98 43702 2242 98.52 0.1853 0.1836 0.1838 0.2165 0.2166 45.43
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.0487 f_angle_d 0.8474 f_chiral_restr 0.053 f_bond_d 0.0061 f_plane_restr 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4056 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 20
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MOLREP phasing Coot model building