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X-ray crystal structure of OXA-24/40 V130D in complex with ertapenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.1 M TRIS HCL, 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.1 69.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.696 α = 90 b = 102.696 β = 90 c = 85.803 γ = 90
Symmetry Space Group P 41 21 2
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 2016-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1272 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.948 102.696 98.7 0.088 0.095 0.034 0.997 12.3 7.4 33705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.948 1.955 98.5 0.909 0.979 0.359 0.817 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 3PAE 1.95 72.62 31971 1678 98.58 0.1899 0.1881 0.1958 0.223 0.2273 RANDOM 43.455
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] -2.37 -2.37 4.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.68 r_dihedral_angle_4_deg 17.081 r_dihedral_angle_3_deg 16.613 r_dihedral_angle_1_deg 6.211 r_angle_refined_deg 1.802 r_chiral_restr 0.117 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1909 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 35
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction AutoProcess data reduction PHASER phasing