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X-ray crystal structure of OXA-24/40 K84D in complex with imipenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M HEPES, 2% v/v PEG 4000, 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.04 69.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.164 α = 90 b = 102.164 β = 90 c = 85.657 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 2013-02-21 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 2.278 102.164 97.5 0.091 0.097 0.033 18 8.3 20836
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.278 2.285 100 0.617 0.658 0.222 8.4
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 2JC7 2.28 102.16 19742 1069 97.63 0.1874 0.1848 0.1866 0.2357 0.2363 RANDOM 50.131
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] -1.71 -1.71 3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.599 r_dihedral_angle_4_deg 20.162 r_dihedral_angle_3_deg 17.586 r_dihedral_angle_1_deg 5.683 r_angle_refined_deg 1.67 r_chiral_restr 0.128 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 40
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction AutoProcess data reduction