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Apo OXA-48 with fully carbamylated Lys73 at pH 7.5
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 2.29 46.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.003 α = 90 b = 106.976 β = 90 c = 124.611 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 EIGER X 16M 2021-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.815342 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 1.92 53.84 99.9 0.994 5.8 12 85231
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 1.92 1.96 0.588 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 1.92 53.84 85147 4389 99.862 0.22 0.2184 0.2156 0.2495 0.2482 24.047
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] 3.04 -0.748 -2.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.889 r_dihedral_angle_4_deg 14.962 r_dihedral_angle_3_deg 13.8 r_dihedral_angle_1_deg 6.325 r_lrange_it 4.26 r_lrange_other 4.214 r_scangle_it 3.312 r_scangle_other 3.312 r_mcangle_it 2.375 r_mcangle_other 2.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.889 r_dihedral_angle_4_deg 14.962 r_dihedral_angle_3_deg 13.8 r_dihedral_angle_1_deg 6.325 r_lrange_it 4.26 r_lrange_other 4.214 r_scangle_it 3.312 r_scangle_other 3.312 r_mcangle_it 2.375 r_mcangle_other 2.375 r_scbond_it 2.119 r_scbond_other 2.119 r_mcbond_it 1.559 r_mcbond_other 1.559 r_angle_refined_deg 1.415 r_angle_other_deg 1.288 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.214 r_nbd_other 0.214 r_symmetry_xyhbond_nbd_refined 0.185 r_symmetry_nbd_other 0.168 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.069 r_ncsr_local_group_4 0.065 r_ncsr_local_group_5 0.064 r_ncsr_local_group_2 0.062 r_ncsr_local_group_3 0.06 r_ncsr_local_group_6 0.054 r_ncsr_local_group_1 0.047 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7932 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing