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OXA-48 with carbamylated Lys73 in complex with bromide ions 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 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 2.28 46.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.568 α = 90 b = 107.263 β = 90 c = 124.62 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 XE 16M 2020-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.918374 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 1.81 81.3 99.9 0.997 7.4 13.3 101237
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 1.81 1.84 0.777 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 1.81 81.3 101119 5098 99.806 0.19 0.1866 0.1842 0.2606 0.2587 27.416
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] 7.054 -3.839 -3.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.712 r_dihedral_angle_4_deg 14.691 r_dihedral_angle_3_deg 13.096 r_rigid_bond_restr 6.553 r_dihedral_angle_1_deg 6.382 r_lrange_it 5.036 r_lrange_other 4.953 r_scangle_it 4.607 r_scangle_other 4.601 r_mcangle_it 4.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.712 r_dihedral_angle_4_deg 14.691 r_dihedral_angle_3_deg 13.096 r_rigid_bond_restr 6.553 r_dihedral_angle_1_deg 6.382 r_lrange_it 5.036 r_lrange_other 4.953 r_scangle_it 4.607 r_scangle_other 4.601 r_mcangle_it 4.159 r_mcangle_other 4.159 r_scbond_it 3.872 r_scbond_other 3.869 r_mcbond_it 3.495 r_mcbond_other 3.493 r_angle_refined_deg 1.49 r_angle_other_deg 1.383 r_symmetry_nbd_refined 0.277 r_nbd_other 0.232 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.193 r_symmetry_nbd_other 0.187 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_other 0.082 r_ncsr_local_group_2 0.077 r_ncsr_local_group_4 0.076 r_ncsr_local_group_3 0.075 r_chiral_restr 0.073 r_ncsr_local_group_5 0.073 r_symmetry_nbtor_other 0.072 r_ncsr_local_group_6 0.072 r_ncsr_local_group_1 0.063 r_bond_refined_d 0.01 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7989 Nucleic Acid Atoms Solvent Atoms 708 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing