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X-ray crystal structure of OXA-24/40 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 = 102.808 α = 90 b = 102.808 β = 90 c = 84.38 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 CCD RAYONIX MX-300 2016-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
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 1.528 84.38 99.6 0.052 0.056 0.019 1 21.9 8.1 68587
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 1.528 1.533 95.7 0.877 0.935 0.321 0.868 8.2
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 1.53 65.31 64876 3365 99.54 0.1733 0.1723 0.1814 0.193 0.2031 RANDOM 25.838
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] -1.55 -1.55 3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.038 r_dihedral_angle_4_deg 18.732 r_dihedral_angle_3_deg 12.915 r_dihedral_angle_1_deg 5.592 r_angle_refined_deg 2.09 r_chiral_restr 0.145 r_bond_refined_d 0.016 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1915 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction AutoProcess data reduction