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OXA-48 with carbamylated Lys73 in complex with hydrolysed Imipenem and bromide ion competing for binding with Arg250 at neutral pH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S2P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 HEPES pH 7.5 no Cl-, 11.6% PEG8000, 8% 1-BuOH mixed with the 10 mg/mL protein stock at 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.37 48.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.31 α = 90 b = 105.965 β = 90 c = 124.679 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 X 16M 2020-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.918381 Diamond I04
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 1.53 80.74 98.3 0.999 12 13.6 159414
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 1.53 1.56 0.62 1.1
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.53 62.417 159336 7990 98.133 0.149 0.1463 0.1988 0.1701 21.078
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] 2.363 -0.705 -1.659
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.462 r_dihedral_angle_4_deg 15.495 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 6.012 r_lrange_it 3.4 r_scangle_it 3.202 r_scangle_other 3.201 r_lrange_other 3.196 r_scbond_it 2.765 r_scbond_other 2.765
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.462 r_dihedral_angle_4_deg 15.495 r_dihedral_angle_3_deg 12.638 r_dihedral_angle_1_deg 6.012 r_lrange_it 3.4 r_scangle_it 3.202 r_scangle_other 3.201 r_lrange_other 3.196 r_scbond_it 2.765 r_scbond_other 2.765 r_mcangle_it 2.252 r_mcangle_other 2.252 r_rigid_bond_restr 1.982 r_mcbond_it 1.859 r_mcbond_other 1.85 r_angle_refined_deg 1.474 r_angle_other_deg 1.443 r_symmetry_nbd_refined 0.293 r_nbd_refined 0.239 r_nbd_other 0.198 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.138 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8012 Nucleic Acid Atoms Solvent Atoms 1019 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing