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Crystal Structure of P. aeruginosa WaaG in complex with UDP-GalNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IV7 2IV7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M MIB pH 4.0, 25% w/v PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.56 51.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.762 α = 90 b = 109.963 β = 90.22 c = 94.326 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 EIGER2 XE 16M 2021-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 55.042 99.9 0.991 5.5 4.9 43178
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 0.554
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 2IV7 2.2 55.04 40977 2152 99.76 0.22105 0.21898 0.2237 0.25814 0.2611 RANDOM 38.501
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] -1.53 -0.67 1.18 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.001 r_dihedral_angle_2_deg 9.561 r_long_range_B_refined 7.714 r_long_range_B_other 7.714 r_dihedral_angle_1_deg 6.866 r_scangle_other 5.835 r_mcangle_it 4.616 r_mcangle_other 4.615 r_scbond_it 3.945 r_scbond_other 3.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.001 r_dihedral_angle_2_deg 9.561 r_long_range_B_refined 7.714 r_long_range_B_other 7.714 r_dihedral_angle_1_deg 6.866 r_scangle_other 5.835 r_mcangle_it 4.616 r_mcangle_other 4.615 r_scbond_it 3.945 r_scbond_other 3.944 r_mcbond_it 3.289 r_mcbond_other 3.289 r_angle_refined_deg 1.537 r_angle_other_deg 0.521 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5781 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing