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Crystal Structure of Wild Type 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 8.3 292 Protein: 7.6 mg/ml, 0.01M Tris pH 8.3, 5mM DDT;
Screen: PEG's II (F8), 0.1 M Sodium acetate, 25% (w/v) PEG 4000, 8% (w/v) Isopropanol
Crystal Properties Matthews coefficient Solvent content 2.39 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.332 α = 90 b = 93.261 β = 90 c = 138.053 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 2019-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.8 30 100 0.07 0.07 0.076 0.03 24.6 6.2 102923 -3 23.7
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 1.8 1.83 100 0.793 0.793 0.864 0.34 0.756 2.5 6.2
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 1.8 29.66 97282 5203 99.95 0.1779 0.1762 0.1824 0.2088 0.2109 RANDOM 30.952
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] -0.11 -0.56 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.605 r_dihedral_angle_4_deg 9.774 r_dihedral_angle_3_deg 8.785 r_dihedral_angle_1_deg 3.143 r_angle_refined_deg 1.234 r_angle_other_deg 0.344 r_chiral_restr 0.063 r_gen_planes_refined 0.055 r_gen_planes_other 0.051 r_bond_refined_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.605 r_dihedral_angle_4_deg 9.774 r_dihedral_angle_3_deg 8.785 r_dihedral_angle_1_deg 3.143 r_angle_refined_deg 1.234 r_angle_other_deg 0.344 r_chiral_restr 0.063 r_gen_planes_refined 0.055 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 8127 Nucleic Acid Atoms Solvent Atoms 968 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing