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OXA-48 with carbamylated Lys73 in complex with iodide 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 291 0.1M HEPES pH 8.0, 10% PEG 8000, 10% 1-BUTANOL mixed with the 10 mg/mL protein stock in 0.1M HEPES pH 7.5 buffer at 1:1 ratio
Crystal Properties Matthews coefficient Solvent content 2.69 54.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.764 α = 90 b = 126.86 β = 98.354 c = 111.1 γ = 90
Symmetry Space Group P 1 21 1
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 2020-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979150 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 1.67 19.78 99.9 0.996 11 6.8 147826
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 1.67 1.7 0.646 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 1.67 19.741 147791 7450 99.849 0.168 0.166 0.1966 0.1894 24.36
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] 3.098 0.985 -2.398 -0.948
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_4_deg 17.041 r_dihedral_angle_3_deg 12.465 r_dihedral_angle_1_deg 5.869 r_lrange_it 5.73 r_lrange_other 5.531 r_scangle_it 4.454 r_scangle_other 4.454 r_scbond_it 2.875 r_scbond_other 2.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.296 r_dihedral_angle_4_deg 17.041 r_dihedral_angle_3_deg 12.465 r_dihedral_angle_1_deg 5.869 r_lrange_it 5.73 r_lrange_other 5.531 r_scangle_it 4.454 r_scangle_other 4.454 r_scbond_it 2.875 r_scbond_other 2.874 r_mcangle_other 2.501 r_mcangle_it 2.5 r_mcbond_it 1.811 r_mcbond_other 1.808 r_angle_refined_deg 1.602 r_angle_other_deg 1.35 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.163 r_symmetry_nbd_other 0.162 r_nbtor_refined 0.157 r_symmetry_nbd_refined 0.155 r_nbd_other 0.145 r_symmetry_xyhbond_nbd_refined 0.133 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7923 Nucleic Acid Atoms Solvent Atoms 921 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing