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Crystal structure of a S310A mutant of PBP2 from Neisseria gonorrhoeae
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 0.1 M CHES, 40% PEG 600
Crystal Properties Matthews coefficient Solvent content 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.594 α = 90 b = 77.007 β = 92.34 c = 87.889 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 2019-02-22 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 1.71 39.1 98.6 0.069 0.034 0.99 45.9 5.1 63070
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 1.71 1.75 92.6 0.4 0.206 0.904 3
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 FOURIER SYNTHESIS THROUGHOUT 6P53 1.71 39.1 59920 3128 97.89 0.19509 0.19368 0.2022 0.2217 0.2244 RANDOM 36.074
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] 4.24 1.29 -1.95 -2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.897 r_dihedral_angle_4_deg 17.266 r_dihedral_angle_3_deg 13.489 r_dihedral_angle_1_deg 5.997 r_long_range_B_refined 5.028 r_long_range_B_other 5.015 r_scangle_other 3.85 r_mcangle_other 2.685 r_mcangle_it 2.682 r_scbond_it 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.897 r_dihedral_angle_4_deg 17.266 r_dihedral_angle_3_deg 13.489 r_dihedral_angle_1_deg 5.997 r_long_range_B_refined 5.028 r_long_range_B_other 5.015 r_scangle_other 3.85 r_mcangle_other 2.685 r_mcangle_it 2.682 r_scbond_it 2.38 r_scbond_other 2.373 r_mcbond_it 1.799 r_mcbond_other 1.79 r_angle_refined_deg 1.281 r_angle_other_deg 0.758 r_chiral_restr 0.075 r_bond_refined_d 0.008 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 4858 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling FFT phasing