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X-ray crystal structure of OXA-24/40 K84D 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 4.18 70.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.828 α = 90 b = 102.828 β = 90 c = 87.433 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-225 2015-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.58 50 96.1 0.12 0.129 0.047 6.2 7.8 14713
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 2.58 2.67 100 0.648 0.693 0.243 0.947 8.1
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 2.58 46.03 13932 737 96.03 0.2188 0.2155 0.2224 0.2866 0.2878 RANDOM 53.652
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] -4.93 -4.93 9.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.396 r_dihedral_angle_3_deg 18.038 r_dihedral_angle_4_deg 16.699 r_dihedral_angle_1_deg 6.514 r_angle_refined_deg 1.946 r_chiral_restr 0.126 r_angle_other_deg 0.01 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1893 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 33
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction