☰ Navigation Tabs
Crystal structure of the transpeptidase domain of a T498A mutant of PBP2 from Neisseria gonorrhoeae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.3 291 0.1 M CHES, 40% PEG600
Crystal Properties Matthews coefficient Solvent content 2 38.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.922 α = 90 b = 77.018 β = 90.55 c = 87.172 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 2019-02-06 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 1.92 34.01 96 0.135 0.062 0.993 23.2 5.3 41093 25.8
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 1.92 1.95 97.4 0.741 0.383 0.708 2.1 4.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.92 34.01 39181 1895 95.77 0.187 0.185 0.234 0.234 RANDOM 31.5
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] 0.05 -2.03 -1 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.352 r_dihedral_angle_4_deg 16.075 r_dihedral_angle_3_deg 14.261 r_dihedral_angle_1_deg 6.039 r_long_range_B_refined 5.085 r_long_range_B_other 5.027 r_scangle_other 3.539 r_mcangle_other 2.619 r_mcangle_it 2.617 r_scbond_it 2.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.352 r_dihedral_angle_4_deg 16.075 r_dihedral_angle_3_deg 14.261 r_dihedral_angle_1_deg 6.039 r_long_range_B_refined 5.085 r_long_range_B_other 5.027 r_scangle_other 3.539 r_mcangle_other 2.619 r_mcangle_it 2.617 r_scbond_it 2.155 r_scbond_other 2.146 r_mcbond_it 1.675 r_mcbond_other 1.67 r_angle_refined_deg 1.281 r_angle_other_deg 0.761 r_chiral_restr 0.076 r_bond_refined_d 0.008 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 4759 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling FFT phasing