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Acetyllysine73-incorporated OXA-48 complexed with imipenem 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 2.42 49.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.799 α = 90 b = 104.995 β = 90 c = 124.745 γ = 90
Symmetry Space Group P 2 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 EIGER X 16M 2021-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976292 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 1.8 62.37 100 0.997 9.9 11.4 55552
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 1.8 1.84 0.588 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 1.8 62.37 55487 2745 99.993 0.18 0.1778 0.1786 0.2137 0.2153 25.438
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] 1.471 0.782 -2.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_dihedral_angle_4_deg 19.264 r_dihedral_angle_3_deg 13.434 r_dihedral_angle_1_deg 6.301 r_lrange_it 5.75 r_lrange_other 5.693 r_scangle_it 4.728 r_scangle_other 4.717 r_scbond_it 3.069 r_scbond_other 3.063
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_dihedral_angle_4_deg 19.264 r_dihedral_angle_3_deg 13.434 r_dihedral_angle_1_deg 6.301 r_lrange_it 5.75 r_lrange_other 5.693 r_scangle_it 4.728 r_scangle_other 4.717 r_scbond_it 3.069 r_scbond_other 3.063 r_mcangle_it 2.87 r_mcangle_other 2.87 r_mcbond_it 2.022 r_mcbond_other 2.018 r_angle_refined_deg 1.539 r_angle_other_deg 1.395 r_nbd_refined 0.213 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.171 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_other 0.122 r_symmetry_nbd_refined 0.119 r_ncsr_local_group_1 0.106 r_symmetry_xyhbond_nbd_refined 0.096 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.01 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 3975 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing