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Crystal structure of the transpeptidase domain of a S310A mutant of PBP2 from Neisseria gonorrhoeae strain H041
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 = 50.487 α = 90 b = 61.079 β = 90 c = 109.419 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 2023-02-21 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 1.9 45.9 96.6 0.107 0.116 0.045 0.991 20.1 5.9 27372 20.4
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 1.93 99.4 0.491 0.533 0.204 0.908 2.75 6.3
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 45.88 25188 1275 96.55 0.177 0.175 0.1749 0.211 0.2111 RANDOM 25.9
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] -2.99 1.26 1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.331 r_dihedral_angle_4_deg 19.958 r_dihedral_angle_3_deg 13.493 r_dihedral_angle_1_deg 6.487 r_long_range_B_refined 6.192 r_scbond_it 3.504 r_mcangle_it 2.835 r_mcbond_it 2.167 r_angle_refined_deg 1.7 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.331 r_dihedral_angle_4_deg 19.958 r_dihedral_angle_3_deg 13.493 r_dihedral_angle_1_deg 6.487 r_long_range_B_refined 6.192 r_scbond_it 3.504 r_mcangle_it 2.835 r_mcbond_it 2.167 r_angle_refined_deg 1.7 r_chiral_restr 0.109 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2423 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing