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X-ray crystal structure of Acinetobacter baumanii beta-lactamase variant OXA-82 K83D in complex with doripenem
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KZH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.09 M HEPES, pH 7.5, 1.26 M Sodium Citrate, 10% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.284 α = 90 b = 70.284 β = 90 c = 448.355 γ = 120
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 2016-06-30 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) 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 1.78 50 99.5 0.976 34.2 6.1 235628
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.84 100 0.873 2 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.78 38.58 197119 10377 87.64 0.15591 0.1546 0.1669 0.18098 0.1924 RANDOM 25.989
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] -0.24 -0.12 -0.24 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.064 r_dihedral_angle_3_deg 14.14 r_dihedral_angle_4_deg 13.747 r_long_range_B_other 8.684 r_long_range_B_refined 8.683 r_scangle_other 7.261 r_dihedral_angle_1_deg 6.492 r_scbond_other 5.861 r_scbond_it 5.86 r_mcangle_it 3.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.064 r_dihedral_angle_3_deg 14.14 r_dihedral_angle_4_deg 13.747 r_long_range_B_other 8.684 r_long_range_B_refined 8.683 r_scangle_other 7.261 r_dihedral_angle_1_deg 6.492 r_scbond_other 5.861 r_scbond_it 5.86 r_mcangle_it 3.261 r_mcangle_other 3.261 r_mcbond_it 2.565 r_mcbond_other 2.565 r_angle_refined_deg 1.329 r_angle_other_deg 1.324 r_chiral_restr 0.068 r_gen_planes_refined 0.017 r_gen_planes_other 0.01 r_bond_refined_d 0.006 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15060 Nucleic Acid Atoms Solvent Atoms 1501 Heterogen Atoms 310
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing