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Crystal Structure of P. aeruginosa WaaG in complex with UDP-glucose
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 0.06M Divalents, 0.1M Buffer System 3 pH 8.5, 30.0% v/v P500MME_P20K
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.633 α = 90 b = 94.426 β = 101.41 c = 70.17 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 2021-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 MAX IV BioMAX
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 1.95 57.551 99.9 0.979 10 3.4 182700
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 1.95 2 0.979
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 1.95 57.54 51684 2794 99.79 0.18173 0.1797 0.1899 0.21905 0.2289 RANDOM 16.148
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] 0.21 -0.85 0.7 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.756 r_dihedral_angle_1_deg 5.785 r_dihedral_angle_2_deg 3.541 r_long_range_B_refined 3.443 r_long_range_B_other 3.08 r_scangle_other 1.383 r_mcangle_it 1.139 r_mcangle_other 1.139 r_angle_refined_deg 0.87 r_scbond_it 0.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.756 r_dihedral_angle_1_deg 5.785 r_dihedral_angle_2_deg 3.541 r_long_range_B_refined 3.443 r_long_range_B_other 3.08 r_scangle_other 1.383 r_mcangle_it 1.139 r_mcangle_other 1.139 r_angle_refined_deg 0.87 r_scbond_it 0.814 r_scbond_other 0.814 r_mcbond_it 0.658 r_mcbond_other 0.655 r_angle_other_deg 0.312 r_chiral_restr 0.044 r_gen_planes_refined 0.004 r_bond_refined_d 0.002 r_bond_other_d 0.002 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 5822 Nucleic Acid Atoms Solvent Atoms 647 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing