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OXA-48 with carbamylated Lys73 in complex with bicarbonate 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 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.807 α = 90 b = 106.404 β = 90 c = 124.706 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 0.976254 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 1.97 81.81 100 0.995 6 13.2 77632
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 1.97 2.01 0.582 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4S2P 1.97 68.496 77539 3748 99.981 0.2 0.1954 0.2861 0.2554 25.536
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] -1.123 -0.957 2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.024 r_dihedral_angle_4_deg 18.049 r_dihedral_angle_3_deg 13.572 r_rigid_bond_restr 9.944 r_lrange_it 6.67 r_lrange_other 6.582 r_dihedral_angle_1_deg 6.494 r_scangle_it 5.806 r_scangle_other 5.793 r_mcangle_it 5.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.024 r_dihedral_angle_4_deg 18.049 r_dihedral_angle_3_deg 13.572 r_rigid_bond_restr 9.944 r_lrange_it 6.67 r_lrange_other 6.582 r_dihedral_angle_1_deg 6.494 r_scangle_it 5.806 r_scangle_other 5.793 r_mcangle_it 5.295 r_mcangle_other 5.294 r_scbond_it 4.803 r_scbond_other 4.798 r_mcbond_it 4.215 r_mcbond_other 4.209 r_angle_refined_deg 1.466 r_angle_other_deg 1.327 r_symmetry_nbd_refined 0.314 r_nbd_other 0.249 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.184 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.075 r_ncsr_local_group_2 0.072 r_ncsr_local_group_4 0.072 r_chiral_restr 0.07 r_ncsr_local_group_3 0.066 r_ncsr_local_group_5 0.064 r_ncsr_local_group_6 0.057 r_symmetry_xyhbond_nbd_other 0.055 r_ncsr_local_group_1 0.045 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8029 Nucleic Acid Atoms Solvent Atoms 614 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing