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Crystal Structure of the Class D Beta-lactamase OXA-935 from Pseudomonas aeruginosa, Monoclinic Crystal Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 Protein: 6.0 mg/ml, 0.01M Tris pH 8.3;
Screen - Classics II (G9): 0.2M Ammonium acetate, 0.1M Tris pH 8.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.074 α = 90 b = 75.043 β = 91.93 c = 82.746 γ = 90
Symmetry Space Group P 1 21 1
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 9M Be 2020-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12713 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.3 30 91.2 0.072 0.079 0.033 0.997 20.6 5.6 126515 -3 10.6
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 1.3 1.32 74 0.517 0.517 0.575 0.247 0.854 3.3 4.9
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 1E3U 1.3 23.95 119981 6069 91.31 0.1502 0.1492 0.1541 0.1699 0.1733 RANDOM 15.778
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] 0.42 -1.17 0.09 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.736 r_dihedral_angle_4_deg 12.682 r_dihedral_angle_3_deg 9.189 r_dihedral_angle_1_deg 3.825 r_angle_refined_deg 1.287 r_rigid_bond_restr 0.694 r_angle_other_deg 0.327 r_chiral_restr 0.062 r_gen_planes_refined 0.056 r_gen_planes_other 0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.736 r_dihedral_angle_4_deg 12.682 r_dihedral_angle_3_deg 9.189 r_dihedral_angle_1_deg 3.825 r_angle_refined_deg 1.287 r_rigid_bond_restr 0.694 r_angle_other_deg 0.327 r_chiral_restr 0.062 r_gen_planes_refined 0.056 r_gen_planes_other 0.049 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3881 Nucleic Acid Atoms Solvent Atoms 725 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing