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Crystal structure of OXA-10 variant A124T in the complex with ceftazidime
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 20% PEG 3350, 0.2 M Sodium formate, 0.1 M Tris-HCl pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.75 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.51 α = 90 b = 99.04 β = 90 c = 127.1 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 PILATUS 6M 2023-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.97942 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.19 29.3 99.61 0.144 0.151 0.042 0.999 15.63 12.6 32211
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.19 2.27 0.317
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FOF 2.19 29.3 30601 1611 99.62 0.16909 0.1669 0.1743 0.20926 0.2144 RANDOM 41.067
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.492 r_long_range_B_refined 10.303 r_long_range_B_other 10.235 r_scangle_other 7.587 r_dihedral_angle_1_deg 6.512 r_dihedral_angle_2_deg 6.43 r_mcangle_other 5.258 r_mcangle_it 5.257 r_scbond_it 4.889 r_scbond_other 4.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.492 r_long_range_B_refined 10.303 r_long_range_B_other 10.235 r_scangle_other 7.587 r_dihedral_angle_1_deg 6.512 r_dihedral_angle_2_deg 6.43 r_mcangle_other 5.258 r_mcangle_it 5.257 r_scbond_it 4.889 r_scbond_other 4.888 r_mcbond_it 3.703 r_mcbond_other 3.691 r_angle_refined_deg 1.769 r_angle_other_deg 0.599 r_chiral_restr 0.084 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3994 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling HKL-3000 phasing PDB_EXTRACT data extraction