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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-6752
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 2.4 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.464 α = 90 b = 60.224 β = 90 c = 110.34 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 2020-10-17 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 2.6 38.7 98.9 0.199 0.215 0.08 0.988 14.1 7.2 10571 29.1
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 2.6 2.7 94.3 0.713 0.769 0.283 0.831 4.2 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 THROUGHOUT 2.613 38.68 10570 514 98.85 0.178 0.1749 0.2319 0.21 RANDOM 28.8
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] 0.113 -0.149 0.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.555 r_dihedral_angle_3_deg 14.713 r_dihedral_angle_2_deg 7.623 r_dihedral_angle_1_deg 7.545 r_lrange_it 6.334 r_lrange_other 6.333 r_scangle_it 4.874 r_scangle_other 4.872 r_mcangle_it 3.916 r_mcangle_other 3.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.555 r_dihedral_angle_3_deg 14.713 r_dihedral_angle_2_deg 7.623 r_dihedral_angle_1_deg 7.545 r_lrange_it 6.334 r_lrange_other 6.333 r_scangle_it 4.874 r_scangle_other 4.872 r_mcangle_it 3.916 r_mcangle_other 3.914 r_scbond_it 3.155 r_scbond_other 3.155 r_mcbond_other 2.504 r_mcbond_it 2.503 r_angle_refined_deg 1.57 r_angle_other_deg 0.518 r_nbd_other 0.218 r_nbd_refined 0.217 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.149 r_xyhbond_nbd_refined 0.102 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_bond_refined_d 0.008 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 2450 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction FFT phasing