7VYY

The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VGV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.2 M Potassium/Sodium tartrate, 0.1 M Bis Tris-propane pH 7.5, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.9858.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.349α = 90
b = 106.052β = 124.87
c = 94.343γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2018-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.4425.4585.90.05526.63.928957
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.442.550.055

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE1VGV2.44325.44928957151085.8850.230.22770.272241.884
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]
0.81-0.229-0.053-0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.045
r_dihedral_angle_4_deg17.367
r_dihedral_angle_3_deg17.257
r_lrange_it6.446
r_lrange_other6.441
r_dihedral_angle_1_deg6.168
r_scangle_it3.623
r_scangle_other3.623
r_mcangle_it3.571
r_mcangle_other3.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.045
r_dihedral_angle_4_deg17.367
r_dihedral_angle_3_deg17.257
r_lrange_it6.446
r_lrange_other6.441
r_dihedral_angle_1_deg6.168
r_scangle_it3.623
r_scangle_other3.623
r_mcangle_it3.571
r_mcangle_other3.57
r_mcbond_it2.153
r_mcbond_other2.153
r_scbond_it2.119
r_scbond_other2.118
r_angle_refined_deg1.313
r_angle_other_deg1.141
r_symmetry_xyhbond_nbd_refined0.218
r_nbd_other0.217
r_symmetry_nbd_other0.192
r_xyhbond_nbd_refined0.189
r_nbd_refined0.179
r_nbtor_refined0.14
r_symmetry_nbd_refined0.132
r_ncsr_local_group_10.116
r_metal_ion_refined0.111
r_symmetry_nbtor_other0.08
r_xyhbond_nbd_other0.071
r_symmetry_xyhbond_nbd_other0.064
r_chiral_restr0.052
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5418
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing