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Crystal structure of the K84D mutant of OXA-24/40 in complex with doripenem
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 8.5 298 100 mM TRIS-HCl, 2.0 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.04 69.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.334 α = 90 b = 102.334 β = 90 c = 85.45 γ = 90
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 MARMOSAIC 300 mm CCD 2009-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 50 98.8 50780
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 94.2
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 2JC7 2.1 31.68 48197 2574 98.5 0.191 0.189 0.1902 0.231 0.2317 RANDOM 37.42
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] -2.18 -2.18 4.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.826 r_dihedral_angle_3_deg 17.655 r_dihedral_angle_4_deg 16.466 r_dihedral_angle_1_deg 5.347 r_scangle_it 4.251 r_scbond_it 2.557 r_mcangle_it 1.612 r_angle_refined_deg 1.522 r_mcbond_it 0.866 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.826 r_dihedral_angle_3_deg 17.655 r_dihedral_angle_4_deg 16.466 r_dihedral_angle_1_deg 5.347 r_scangle_it 4.251 r_scbond_it 2.557 r_mcangle_it 1.612 r_angle_refined_deg 1.522 r_mcbond_it 0.866 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3858 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 69
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling