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Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing seven resistance mutations and three epistatic mutations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.3 291 40% PEG 600, 0.1M CHES
Crystal Properties Matthews coefficient Solvent content 2.08 40.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.344 α = 90 b = 79.594 β = 90.45 c = 81.369 γ = 90
Symmetry Space Group P 1 21 1
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 2019-06-20 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) 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 1.46 36.25 99.4 0.075 0.08 0.029 0.992 9.7 7.4 99246
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 1.46 1.49 91.1 0.441 0.482 0.189 0.931 5.5
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 1.46 36.25 94207 5009 99.44 0.16315 0.16172 0.1616 0.18793 0.1878 RANDOM 21.7
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] -0.37 -0.09 1.78 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.694 r_dihedral_angle_2_deg 7.179 r_dihedral_angle_1_deg 6.852 r_long_range_B_refined 5.817 r_long_range_B_other 5.786 r_scangle_other 4.572 r_scbond_it 3.071 r_scbond_other 3.071 r_mcangle_it 2.397 r_mcangle_other 2.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.694 r_dihedral_angle_2_deg 7.179 r_dihedral_angle_1_deg 6.852 r_long_range_B_refined 5.817 r_long_range_B_other 5.786 r_scangle_other 4.572 r_scbond_it 3.071 r_scbond_other 3.071 r_mcangle_it 2.397 r_mcangle_other 2.397 r_angle_refined_deg 1.976 r_mcbond_it 1.713 r_mcbond_other 1.712 r_angle_other_deg 0.67 r_chiral_restr 0.104 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 4872 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PDB_EXTRACT data extraction REFMAC phasing