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Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing seven resistance 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, 0.1 M CHES
Crystal Properties Matthews coefficient Solvent content 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.556 α = 90 b = 76.839 β = 92.37 c = 87.478 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 PIXEL DECTRIS EIGER X 16M 2019-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 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 1.9 50 98.9 0.087 0.095 0.036 0.986 10.4 6.7 46263
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 1.9 1.97 99.7 0.535 0.583 0.227 0.875 3.6 6.5
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 1.9 35.75 44090 2155 98.4 0.2017 0.19985 0.2042 0.23883 0.2438 RANDOM 52.3
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] -2.47 -2.64 -3.17 5.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.49 r_long_range_B_refined 9.402 r_long_range_B_other 9.391 r_dihedral_angle_2_deg 8.501 r_dihedral_angle_1_deg 7.219 r_scangle_other 4.096 r_mcangle_it 2.97 r_mcangle_other 2.97 r_scbond_it 2.631 r_scbond_other 2.611
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.49 r_long_range_B_refined 9.402 r_long_range_B_other 9.391 r_dihedral_angle_2_deg 8.501 r_dihedral_angle_1_deg 7.219 r_scangle_other 4.096 r_mcangle_it 2.97 r_mcangle_other 2.97 r_scbond_it 2.631 r_scbond_other 2.611 r_mcbond_it 2.061 r_mcbond_other 2.059 r_angle_refined_deg 1.739 r_angle_other_deg 0.618 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 4882 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PDB_EXTRACT data extraction REFMAC phasing