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Crystal Structure of K83A 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 7.5 292 Protein: 7.5 mg/ml, 0.01M Tris pH 8.3, 5mM DDT;
Screen: PEGSs II (D1), 0.1M Sodium acetate, 0.1M HEPES pH 7.5, 22% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.534 α = 90 b = 93.621 β = 90 c = 138.067 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 1.88 30 100 0.068 0.068 0.074 0.028 26.7 6.9 90491 -3 26.8
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 1.88 1.91 100 0.79 0.79 0.853 0.321 0.779 2.5 7
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 1.88 29.71 85969 4441 99.77 0.1699 0.1684 0.1755 0.1978 0.2023 RANDOM 33.134
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 -1.25 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.764 r_dihedral_angle_4_deg 12.71 r_dihedral_angle_3_deg 9.754 r_dihedral_angle_1_deg 3.698 r_angle_refined_deg 1.261 r_angle_other_deg 0.345 r_chiral_restr 0.062 r_gen_planes_refined 0.055 r_gen_planes_other 0.051 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.764 r_dihedral_angle_4_deg 12.71 r_dihedral_angle_3_deg 9.754 r_dihedral_angle_1_deg 3.698 r_angle_refined_deg 1.261 r_angle_other_deg 0.345 r_chiral_restr 0.062 r_gen_planes_refined 0.055 r_gen_planes_other 0.051 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8114 Nucleic Acid Atoms Solvent Atoms 886 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing