7PJI

Crystal structure of Pseudomonas aeruginosa guaB (IMP dehydrogenase) bound to ATP and GDP at 1.65A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AVF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295Condition D11 of the commercial screening Morpheus (Gorrec, 2009): 0.02M Sodium formate; 0.02M Ammonium acetate; 0.02M Sodium citrate tribasic dihydrate; 0.02M Potassium sodium tartrate tetrahydrate; 0.02M Sodium oxamate, 12.5% v/v MPD; 12.5% PEG 1000; 12.5% w/v PEG 3350 in 0.1M of the buffer system Tris (base), bicine, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.8156.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.947α = 90
b = 120.947β = 90
c = 145.487γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I041.000008DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.6550.767.80.090.0940.0250.99913.1813.98486125.18
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.717.091.761.8270.4890.2870.3913.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4AVF1.6550.71.3484628428667.80.17340.17230.195335.28
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.4368
f_angle_d1.0459
f_chiral_restr0.0579
f_bond_d0.0068
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6416
Nucleic Acid Atoms
Solvent Atoms647
Heterogen Atoms184

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing