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Acetyllysine73-incorporated OXA-48 complexed with oxacillin
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 2.44 49.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.83 α = 90 b = 105.48 β = 90 c = 124.96 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 0.976270 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 2.32 53.76 99.3 0.996 7 10.9 26329
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 2.32 2.4 0.566 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 2.32 53.76 26280 1266 99.215 0.238 0.2352 0.2361 0.2886 0.2902 46.938
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] 4.801 -0.452 -4.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.754 r_dihedral_angle_3_deg 16.295 r_dihedral_angle_4_deg 14.331 r_lrange_it 8.528 r_lrange_other 8.528 r_dihedral_angle_1_deg 7.153 r_mcangle_it 6.128 r_mcangle_other 6.128 r_scangle_it 5.765 r_scangle_other 5.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.754 r_dihedral_angle_3_deg 16.295 r_dihedral_angle_4_deg 14.331 r_lrange_it 8.528 r_lrange_other 8.528 r_dihedral_angle_1_deg 7.153 r_mcangle_it 6.128 r_mcangle_other 6.128 r_scangle_it 5.765 r_scangle_other 5.764 r_mcbond_other 3.957 r_mcbond_it 3.956 r_scbond_it 3.614 r_scbond_other 3.613 r_angle_refined_deg 1.529 r_angle_other_deg 1.195 r_nbd_refined 0.214 r_nbd_other 0.189 r_symmetry_nbd_other 0.179 r_symmetry_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.128 r_chiral_restr_other 0.125 r_symmetry_nbd_refined 0.122 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_1 0.074 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3958 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement SADABS data reduction Aimless data scaling MOLREP phasing