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Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with cefoperazone
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 32-40% PEG 600, 0.1 M CHES
Crystal Properties Matthews coefficient Solvent content 2.3 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.618 α = 90 b = 61.436 β = 90 c = 109.994 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 EIGER2 S 16M 2022-03-06 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 1.8 46.03 99.8 0.104 0.112 0.04 0.996 18.9 7.2 32541 9
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 1.8 1.83 99.7 0.401 0.432 0.157 0.916 3.2 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 (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 1.8 46.03 30917 1563 99.72 0.174 0.173 0.1837 0.201 0.2074 RANDOM 14.2
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] -0.23 0.24 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.978 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_3_deg 12.413 r_dihedral_angle_1_deg 6.82 r_long_range_B_refined 4.527 r_long_range_B_other 4.493 r_scangle_other 3.359 r_mcangle_it 2.114 r_mcangle_other 2.113 r_scbond_it 2.032
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.978 r_dihedral_angle_4_deg 16.759 r_dihedral_angle_3_deg 12.413 r_dihedral_angle_1_deg 6.82 r_long_range_B_refined 4.527 r_long_range_B_other 4.493 r_scangle_other 3.359 r_mcangle_it 2.114 r_mcangle_other 2.113 r_scbond_it 2.032 r_scbond_other 2.031 r_angle_refined_deg 1.682 r_angle_other_deg 1.399 r_mcbond_it 1.317 r_mcbond_other 1.313 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2453 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing