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Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin decreased susceptibility strain 35/02
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 2.42 49.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.621 α = 90 b = 61.085 β = 90 c = 109.14 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 EIGER X 16M 2019-10-05 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) 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 1.93 31.72 99.5 0.137 0.05 0.997 35.7 8.7 26212
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 1.93 1.96 99.8 0.979 0.349 0.658 7.2 9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 6P53 1.93 31.72 24878 1293 99.53 0.18407 0.18296 0.1893 0.20532 0.2065 RANDOM 35.133
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] -0.27 -0.28 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.404 r_dihedral_angle_4_deg 13.488 r_dihedral_angle_3_deg 12.833 r_dihedral_angle_1_deg 5.722 r_long_range_B_refined 4.891 r_long_range_B_other 4.869 r_scangle_other 3.753 r_mcangle_it 2.407 r_mcangle_other 2.407 r_scbond_it 2.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.404 r_dihedral_angle_4_deg 13.488 r_dihedral_angle_3_deg 12.833 r_dihedral_angle_1_deg 5.722 r_long_range_B_refined 4.891 r_long_range_B_other 4.869 r_scangle_other 3.753 r_mcangle_it 2.407 r_mcangle_other 2.407 r_scbond_it 2.283 r_scbond_other 2.282 r_mcbond_it 1.602 r_mcbond_other 1.588 r_angle_refined_deg 1.202 r_angle_other_deg 0.737 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 2450 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing