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Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041
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 2.41 49.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.429 α = 90 b = 61.329 β = 90 c = 108.961 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 2019-07-01 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 1.55 31.69 98.3 0.118 0.047 0.994 31.8 6.8 48525
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 1.55 1.58 0.625 0.268 0.851 3.1
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 1.55 31.69 46125 2347 97.53 0.17921 0.17817 0.1897 0.20028 0.2067 RANDOM 17.308
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] -0.8 0.11 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.142 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_3_deg 10.987 r_dihedral_angle_1_deg 6.007 r_long_range_B_refined 3.62 r_long_range_B_other 3.531 r_scangle_other 2.217 r_mcangle_it 1.574 r_mcangle_other 1.574 r_scbond_it 1.356
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.142 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_3_deg 10.987 r_dihedral_angle_1_deg 6.007 r_long_range_B_refined 3.62 r_long_range_B_other 3.531 r_scangle_other 2.217 r_mcangle_it 1.574 r_mcangle_other 1.574 r_scbond_it 1.356 r_scbond_other 1.355 r_angle_refined_deg 1.291 r_mcbond_it 0.926 r_mcbond_other 0.924 r_angle_other_deg 0.747 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 2453 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling FFT phasing