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Crystal Structure of C79A Mutant of Class D beta-lactamase from Clostridium difficile 630
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UE2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 Protein: 7.2 mg/ml, 0.01M Tris pH 8.3, 5mM DDT;
Screen: PACT (D4), 0.1M MMT buffer pH 7.0, 25% (w/v) PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.118 α = 90 b = 93.878 β = 90 c = 138.346 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 Be 2020-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.95 30 100 0.074 0.074 0.08 0.03 25.1 7.4 82125 -3 31.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.722 0.722 0.776 0.283 0.844 2.9 7.4
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 6ue2 1.95 29.84 78063 3989 99.83 0.1793 0.1778 0.1841 0.2066 0.2091 RANDOM 39.825
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] 0.96 -0.1 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.795 r_dihedral_angle_3_deg 9.136 r_dihedral_angle_4_deg 9.016 r_dihedral_angle_1_deg 3.134 r_angle_refined_deg 1.242 r_angle_other_deg 0.339 r_chiral_restr 0.061 r_gen_planes_refined 0.054 r_gen_planes_other 0.051 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.795 r_dihedral_angle_3_deg 9.136 r_dihedral_angle_4_deg 9.016 r_dihedral_angle_1_deg 3.134 r_angle_refined_deg 1.242 r_angle_other_deg 0.339 r_chiral_restr 0.061 r_gen_planes_refined 0.054 r_gen_planes_other 0.051 r_bond_refined_d 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8130 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing