4NEQ

The structure of UDP-GlcNAc 2-epimerase from Methanocaldococcus jannaschii


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP727720% v/v PEG 3350, 300mM potassium iodine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7855.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.947α = 90
b = 67.947β = 90
c = 180.209γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDADSC QUANTUM 315r2013-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.9762NSRRCBL13C1

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
12.85301000.10110.71187822

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT4NES2.8529.5721.3511836119299.930.20170.1940.2708RANDOM
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_d17.81
f_angle_d1.27
f_chiral_restr0.081
f_bond_d0.009
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2871
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms8

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling