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Crystal structure of the transpeptidase domain of a Y422A mutant of PBP2 from Neisseria gonorrhoeae strain H041 acylated by ceftriaxone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 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 = 49.771 α = 90 b = 59.45 β = 90 c = 112.933 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 RAYONIX MX-300 2023-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
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 2.4 50 97.6 0.13 0.052 0.985 8.5 6.9 13460
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 2.4 2.44 90.3 0.341 0.139 0.902 2 5.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2.4 40.98 12720 689 97.18 0.199 0.19 0.1992 0.243 0.2456 RANDOM 35.2
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] -2.97 -1.84 4.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.466 r_long_range_B_refined 7.681 r_long_range_B_other 7.68 r_dihedral_angle_1_deg 7.073 r_scangle_other 6.119 r_dihedral_angle_2_deg 5.603 r_mcangle_it 4.198 r_mcangle_other 4.197 r_scbond_it 3.786 r_scbond_other 3.784
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.466 r_long_range_B_refined 7.681 r_long_range_B_other 7.68 r_dihedral_angle_1_deg 7.073 r_scangle_other 6.119 r_dihedral_angle_2_deg 5.603 r_mcangle_it 4.198 r_mcangle_other 4.197 r_scbond_it 3.786 r_scbond_other 3.784 r_mcbond_it 2.655 r_mcbond_other 2.635 r_angle_refined_deg 1.928 r_angle_other_deg 0.57 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 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 2446 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing