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Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02 in complex with boronate inhibitor VNRX-6884
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.3 291 40% PEG 600, 0.1 M CHES, PH 9.3
Crystal Properties Matthews coefficient Solvent content 2.42 49.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.586 α = 90 b = 60.735 β = 90 c = 110.281 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 2020-10-31 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) 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 1.89 38.9 99.3 0.109 0.117 0.044 0.998 15.9 7.1 27662 22.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.96 96.1 0.708 0.761 0.276 0.839 3.1 7.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.89 38.9 27662 1337 99.3 0.175 0.173 0.205 0.2031 RANDOM 24.3
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] 0.053 -0.038 -0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.611 r_dihedral_angle_3_deg 13.794 r_dihedral_angle_1_deg 6.792 r_dihedral_angle_2_deg 6.544 r_lrange_it 6.387 r_lrange_other 6.376 r_scangle_it 5.066 r_scangle_other 5.065 r_mcangle_other 3.434 r_mcangle_it 3.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.611 r_dihedral_angle_3_deg 13.794 r_dihedral_angle_1_deg 6.792 r_dihedral_angle_2_deg 6.544 r_lrange_it 6.387 r_lrange_other 6.376 r_scangle_it 5.066 r_scangle_other 5.065 r_mcangle_other 3.434 r_mcangle_it 3.433 r_scbond_other 3.269 r_scbond_it 3.268 r_mcbond_it 2.281 r_mcbond_other 2.278 r_angle_refined_deg 1.58 r_angle_other_deg 0.531 r_nbd_refined 0.225 r_symmetry_nbd_other 0.186 r_nbd_other 0.179 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.176 r_symmetry_nbd_refined 0.144 r_xyhbond_nbd_refined 0.138 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2450 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction FFT phasing