8B63

Crystal Structure of P. aeruginosa WaaG in complex with UDP-GalNAc


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2910.1M MIB pH 4.0, 25% w/v PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.5651.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.762α = 90
b = 109.963β = 90.22
c = 94.326γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.255.04299.90.9915.54.943178
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.270.554

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2IV72.255.0440977215299.760.221050.218980.25814RANDOM38.501
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]
-1.53-0.671.180.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.001
r_dihedral_angle_2_deg9.561
r_long_range_B_refined7.714
r_long_range_B_other7.714
r_dihedral_angle_1_deg6.866
r_scangle_other5.835
r_mcangle_it4.616
r_mcangle_other4.615
r_scbond_it3.945
r_scbond_other3.944
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.001
r_dihedral_angle_2_deg9.561
r_long_range_B_refined7.714
r_long_range_B_other7.714
r_dihedral_angle_1_deg6.866
r_scangle_other5.835
r_mcangle_it4.616
r_mcangle_other4.615
r_scbond_it3.945
r_scbond_other3.944
r_mcbond_it3.289
r_mcbond_other3.289
r_angle_refined_deg1.537
r_angle_other_deg0.521
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5781
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing