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Crystal structure of the transpeptidase domain of PBP2 from Neisseria gonorrhoeae strain FA19 acylated by piperacillin
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 291 35-40% PEG 600 and 0.1 M CHES
Crystal Properties Matthews coefficient Solvent content 2.06 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.986 α = 90 b = 77.962 β = 90.75 c = 87.237 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 2022-02-25 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) 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 3.15 39 99 0.128 0.075 0.992 11.9 3.9 10473
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.26 0.668 0.391 0.731 3.3 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 3.15 39 9942 537 98.78 0.159 0.153 0.1596 0.266 0.2683 RANDOM 81.3
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] 10.43 -1.27 -4.26 -6.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.038 r_long_range_B_refined 11.348 r_long_range_B_other 11.347 r_dihedral_angle_1_deg 8.293 r_scangle_other 8 r_mcangle_it 7.872 r_mcangle_other 7.872 r_scbond_it 4.848 r_scbond_other 4.847 r_mcbond_it 4.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.038 r_long_range_B_refined 11.348 r_long_range_B_other 11.347 r_dihedral_angle_1_deg 8.293 r_scangle_other 8 r_mcangle_it 7.872 r_mcangle_other 7.872 r_scbond_it 4.848 r_scbond_other 4.847 r_mcbond_it 4.83 r_mcbond_other 4.83 r_dihedral_angle_2_deg 4.741 r_angle_refined_deg 1.382 r_angle_other_deg 0.473 r_chiral_restr 0.063 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 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 4858 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing