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X-ray crystal structure of OXA-24/40 V130D in complex with imipenem
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 Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.304 α = 90 b = 102.304 β = 90 c = 86.921 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 1.938 66.24 100 0.103 0.111 0.041 0.998 13.9 7.2 34803
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 1.938 1.945 98.5 1.679 1.804 0.655 0.531 7.3
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 1.94 66.24 32880 1688 99.26 0.1989 0.1974 0.2012 0.2279 0.2361 RANDOM 39.278
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] -1.93 -1.93 3.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.169 r_dihedral_angle_4_deg 20.887 r_dihedral_angle_3_deg 16.634 r_dihedral_angle_1_deg 6.041 r_angle_refined_deg 1.923 r_chiral_restr 0.127 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1898 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction AutoProcess data reduction