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X-ray crystal structure of OXA-24/40 V130D in complex with meropenem
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 4.05 69.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.391 α = 90 b = 102.391 β = 90 c = 85.647 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 1.97 102.391 89.4 0.14 0.151 0.054 0.997 12 7.2 29280
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 1.97 1.979 92.5 1.169 1.26 0.461 0.602 7.2
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 3PAE 1.97 102.39 27753 1482 89.47 0.2002 0.1988 0.1979 0.2292 0.2298 RANDOM 46.132
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] -1.82 -1.82 3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.475 r_dihedral_angle_4_deg 20.9 r_dihedral_angle_3_deg 16.268 r_dihedral_angle_1_deg 5.614 r_angle_refined_deg 1.924 r_chiral_restr 0.123 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1900 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 34
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction AutoProcess data reduction PHASER phasing