5G5K

Crystal structure of NagZ from Pseudomonas aeruginosa in complex with the inhibitor 2-acetamido-1,2-dideoxynojirimycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherAPO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1630% PEG 8000 100 MM SODIUM CACODYLATE PH 6.0 200 MM SODIUM ACETATE PH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.1141.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.224α = 90
b = 67.607β = 97.83
c = 74.064γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-FTOROIDAL MIRROR2015-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.97945SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.141.2897.90.115.72.711501172.51
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.3199.90.551.42.8

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTAPO STRUCTURE OF NAGZ FROM PSEUDOMONAS AERUGINOSA3.141.2891.341147533897.690.24010.23870.283871.04
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_d20.133
f_angle_d0.519
f_chiral_restr0.038
f_plane_restr0.004
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5082
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms28

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing