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Acetyllysine73-incorporated OXA-48 complexed with imipenem and bromide ions in both active and inactive acyl-enzyme intermediates
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 0.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.29 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.398 α = 90 b = 161.934 β = 90.513 c = 107.782 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2020-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976269 Diamond I03
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 2.15 80.97 99.6 0.991 7.3 6.7 117282
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 2.15 2.19 0.585 1.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4S2P 2.15 80.97 117142 5895 99.489 0.212 0.2098 0.2102 0.2498 0.2513 42.613
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] -1.92 0.293 4.44 -2.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.154 r_dihedral_angle_4_deg 15.578 r_dihedral_angle_3_deg 13.661 r_lrange_other 8.43 r_lrange_it 8.427 r_dihedral_angle_1_deg 6.603 r_scangle_it 6.19 r_scangle_other 6.19 r_mcangle_it 6.104 r_mcangle_other 6.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.154 r_dihedral_angle_4_deg 15.578 r_dihedral_angle_3_deg 13.661 r_lrange_other 8.43 r_lrange_it 8.427 r_dihedral_angle_1_deg 6.603 r_scangle_it 6.19 r_scangle_other 6.19 r_mcangle_it 6.104 r_mcangle_other 6.104 r_mcbond_it 4.174 r_mcbond_other 4.173 r_scbond_it 4.062 r_scbond_other 4.062 r_angle_refined_deg 1.464 r_angle_other_deg 1.28 r_nbd_other 0.266 r_symmetry_nbd_refined 0.255 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_other 0.075 r_chiral_restr 0.069 r_ncsr_local_group_4 0.069 r_ncsr_local_group_6 0.068 r_ncsr_local_group_2 0.067 r_ncsr_local_group_3 0.063 r_ncsr_local_group_8 0.061 r_ncsr_local_group_23 0.061 r_ncsr_local_group_7 0.059 r_ncsr_local_group_12 0.059 r_ncsr_local_group_5 0.057 r_ncsr_local_group_10 0.057 r_ncsr_local_group_26 0.057 r_ncsr_local_group_11 0.056 r_ncsr_local_group_17 0.056 r_ncsr_local_group_19 0.055 r_ncsr_local_group_21 0.055 r_ncsr_local_group_18 0.053 r_ncsr_local_group_25 0.053 r_ncsr_local_group_13 0.052 r_ncsr_local_group_28 0.052 r_ncsr_local_group_1 0.051 r_ncsr_local_group_9 0.051 r_ncsr_local_group_16 0.051 r_ncsr_local_group_27 0.05 r_ncsr_local_group_14 0.049 r_ncsr_local_group_20 0.048 r_ncsr_local_group_15 0.045 r_ncsr_local_group_24 0.045 r_ncsr_local_group_22 0.041 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15784 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 232
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing