7VZ6

The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in complex with UDP-glucose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.2M lithium sulfate, 0.1M Bis tris pH 5.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3948.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.833α = 74.867
b = 104.941β = 72.918
c = 106.84γ = 68.076
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2019-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1NSRRCTPS 05A

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
12.0921.5695.20.05719.72.2176474
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)
12.12.180.057

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 REPLACEMENTNONE1vgv2.09221.558176474882495.090.2020.20080.227828.96
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]
0.1190.0180.1080.0520.02-0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.758
r_dihedral_angle_4_deg15.456
r_dihedral_angle_3_deg15.3
r_lrange_it7.12
r_lrange_other7.077
r_dihedral_angle_1_deg6.585
r_scangle_it5.225
r_scangle_other5.225
r_mcangle_other3.75
r_mcangle_it3.749
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.758
r_dihedral_angle_4_deg15.456
r_dihedral_angle_3_deg15.3
r_lrange_it7.12
r_lrange_other7.077
r_dihedral_angle_1_deg6.585
r_scangle_it5.225
r_scangle_other5.225
r_mcangle_other3.75
r_mcangle_it3.749
r_scbond_it3.305
r_scbond_other3.305
r_mcbond_it2.532
r_mcbond_other2.53
r_angle_other_deg1.558
r_angle_refined_deg1.495
r_symmetry_nbd_refined0.211
r_nbd_other0.209
r_nbd_refined0.203
r_symmetry_nbd_other0.2
r_xyhbond_nbd_refined0.181
r_metal_ion_refined0.168
r_symmetry_xyhbond_nbd_refined0.167
r_nbtor_refined0.148
r_ncsr_local_group_130.09
r_ncsr_local_group_80.088
r_ncsr_local_group_110.088
r_ncsr_local_group_220.087
r_ncsr_local_group_90.086
r_ncsr_local_group_200.086
r_ncsr_local_group_180.085
r_ncsr_local_group_70.084
r_ncsr_local_group_10.083
r_ncsr_local_group_100.083
r_ncsr_local_group_120.081
r_ncsr_local_group_280.081
r_ncsr_local_group_140.08
r_ncsr_local_group_50.079
r_ncsr_local_group_190.078
r_ncsr_local_group_250.078
r_ncsr_local_group_270.077
r_ncsr_local_group_30.076
r_chiral_restr0.074
r_ncsr_local_group_210.074
r_ncsr_local_group_150.073
r_ncsr_local_group_230.073
r_ncsr_local_group_20.072
r_ncsr_local_group_160.072
r_ncsr_local_group_240.072
r_ncsr_local_group_170.071
r_symmetry_xyhbond_nbd_other0.07
r_ncsr_local_group_260.069
r_ncsr_local_group_40.068
r_ncsr_local_group_60.068
r_symmetry_nbtor_other0.067
r_bond_other_d0.018
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22403
Nucleic Acid Atoms
Solvent Atoms1499
Heterogen Atoms295

Software

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