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OXA-48 with decarbamylated Lys73 in complex with avibactam at pH 8.0
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 8 291 0.1M HEPES,pH=8.0, 10%PEG 8000, 4% 1-butanol, 10mM Avibactam, mixed with the 10 mg/mL protein stock at 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.749 α = 90 b = 107.959 β = 90 c = 125.675 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 CCD ADSC QUANTUM 315r 2019-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979191 SSRF BL17U1
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 1.6 81.89 99.9 0.999 12.1 13.2 160843
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 1.6 1.63 0.747 1.2
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 1.6 73.144 160736 7894 99.847 0.189 0.188 0.1849 0.2157 0.2131 33.332
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] 4.545 -1.869 -2.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.59 r_dihedral_angle_4_deg 17.482 r_dihedral_angle_3_deg 12.999 r_lrange_it 6.297 r_lrange_other 6.241 r_dihedral_angle_1_deg 6.131 r_scangle_it 5.336 r_scangle_other 5.336 r_scbond_it 3.605 r_scbond_other 3.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.59 r_dihedral_angle_4_deg 17.482 r_dihedral_angle_3_deg 12.999 r_lrange_it 6.297 r_lrange_other 6.241 r_dihedral_angle_1_deg 6.131 r_scangle_it 5.336 r_scangle_other 5.336 r_scbond_it 3.605 r_scbond_other 3.598 r_mcangle_it 3.196 r_mcangle_other 3.185 r_mcbond_it 2.411 r_mcbond_other 2.4 r_angle_refined_deg 1.589 r_angle_other_deg 1.438 r_chiral_restr_other 0.226 r_nbd_refined 0.216 r_nbd_other 0.19 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.172 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.149 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7929 Nucleic Acid Atoms Solvent Atoms 692 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing