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Crystal structure of the transpeptidase domain of a Y422F mutant of PBP2 from Neisseria gonorrhoeae strain H041 acylated by cefoperazone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VBD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.1 291 0.1 M CHES buffer, pH 9.1 to 10.1, and 32-42% PEG 600
Crystal Properties Matthews coefficient Solvent content 2.3 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.6 α = 90 b = 61.6 β = 90 c = 110.1 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 EIGER X 16M 2025-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 39.1 92.6 0.181 0.072 0.968 16.5 6.8 10328 35.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 99.6 0.47 0.185 0.909 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS FREE R-VALUE 2.6 39.1 10292 538 92.587 0.23 0.227 0.2304 0.292 0.2922 42.5
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] -0.802 -2.775 3.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.86 r_dihedral_angle_3_deg 13.927 r_dihedral_angle_2_deg 10.546 r_lrange_it 8.08 r_lrange_other 8.078 r_dihedral_angle_1_deg 7.971 r_scangle_it 6.423 r_scangle_other 6.422 r_mcangle_it 5.318 r_mcangle_other 5.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.86 r_dihedral_angle_3_deg 13.927 r_dihedral_angle_2_deg 10.546 r_lrange_it 8.08 r_lrange_other 8.078 r_dihedral_angle_1_deg 7.971 r_scangle_it 6.423 r_scangle_other 6.422 r_mcangle_it 5.318 r_mcangle_other 5.317 r_scbond_it 4.058 r_scbond_other 4.056 r_mcbond_it 3.558 r_mcbond_other 3.539 r_angle_refined_deg 1.7 r_angle_other_deg 1.544 r_nbd_refined 0.216 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.177 r_nbd_other 0.14 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_refined 0.056 r_symmetry_nbd_refined 0.01 r_bond_refined_d 0.007 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 2452 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling FFT phasing