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Crystal structure of the V130D 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 VAPOR DIFFUSION, HANGING DROP 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 4.03 69.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.274 α = 90 b = 102.274 β = 90 c = 85.449 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 2009-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1 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 2.25 50 99 41616
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 2.25 2.33 95.5
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 2.25 50 39512 2097 98.97 0.19127 0.18905 0.1857 0.23298 0.2268 RANDOM 36.791
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] -3.16 -3.16 6.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.279 r_dihedral_angle_4_deg 21.396 r_dihedral_angle_3_deg 17.399 r_dihedral_angle_1_deg 5.602 r_scangle_it 4.948 r_scbond_it 2.942 r_mcangle_it 1.924 r_angle_refined_deg 1.622 r_mcbond_it 1.019 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.279 r_dihedral_angle_4_deg 21.396 r_dihedral_angle_3_deg 17.399 r_dihedral_angle_1_deg 5.602 r_scangle_it 4.948 r_scbond_it 2.942 r_mcangle_it 1.924 r_angle_refined_deg 1.622 r_mcbond_it 1.019 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 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 3874 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 84
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling