☰ Navigation Tabs
Crystal structure of the transpeptidase domain of a Y422F mutant of PBP2 from Neisseria gonorrhoeae strain H041
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 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 = 61.5 β = 90 c = 109.1 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 45.9 99.9 0.154 0.048 0.971 12.6 11.6 10939 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 2.69 99.5 0.401 0.132 0.899 3.8 9.1
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 2.603 45.9 10899 567 99.5 0.191 0.189 0.1893 0.228 0.2306 29.4
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] -3.49 -0.536 4.026
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.326 r_dihedral_angle_6_deg 14.064 r_lrange_it 7.77 r_dihedral_angle_1_deg 7.709 r_dihedral_angle_2_deg 6.143 r_scangle_it 5.82 r_scbond_it 3.617 r_mcangle_it 3.49 r_mcbond_it 2.147 r_angle_refined_deg 1.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.326 r_dihedral_angle_6_deg 14.064 r_lrange_it 7.77 r_dihedral_angle_1_deg 7.709 r_dihedral_angle_2_deg 6.143 r_scangle_it 5.82 r_scbond_it 3.617 r_mcangle_it 3.49 r_mcbond_it 2.147 r_angle_refined_deg 1.538 r_nbtor_refined 0.31 r_symmetry_nbd_refined 0.279 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.118 r_symmetry_xyhbond_nbd_refined 0.103 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2452 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing