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Crystal Structure of P. aeruginosa WaaG in complex with UMP
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 0.2 M Lithium chloride, 0.1 M MES pH 6.0, 20 % PEG6000
Crystal Properties Matthews coefficient Solvent content 2.48 50.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.928 α = 90 b = 108.441 β = 90.11 c = 92.358 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 2021-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 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 2 108.4 96.9 0.911 6.6 3.3 53974
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 2.05 0.36
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 92.36 51278 2666 96.87 0.19663 0.19413 0.2055 0.24461 0.2552 RANDOM 37.409
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] -1.59 0.67 2.14 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.259 r_dihedral_angle_2_deg 9.266 r_long_range_B_other 7.234 r_long_range_B_refined 7.229 r_dihedral_angle_1_deg 6.461 r_scangle_other 5.947 r_scbond_it 4.221 r_scbond_other 4.22 r_mcangle_it 4.196 r_mcangle_other 4.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.259 r_dihedral_angle_2_deg 9.266 r_long_range_B_other 7.234 r_long_range_B_refined 7.229 r_dihedral_angle_1_deg 6.461 r_scangle_other 5.947 r_scbond_it 4.221 r_scbond_other 4.22 r_mcangle_it 4.196 r_mcangle_other 4.195 r_mcbond_it 3.215 r_mcbond_other 3.215 r_angle_refined_deg 1.596 r_angle_other_deg 0.529 r_chiral_restr 0.073 r_bond_refined_d 0.009 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 5842 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing