7VZA

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2M lithium sulfate, 0.1M Bis tris pH5.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3647.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.82α = 74.536
b = 104.77β = 73.051
c = 106.314γ = 68.39
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2020-04-27MSINGLE 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
12.5819.89594.10.0523.82.491395
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)
12.62.680.05

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 REPLACEMENTNONE1VGV2.5819.89591395464493.9460.2120.20980.248845.239
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]
0.417-0.3120.101-0.3710.044-0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.582
r_dihedral_angle_4_deg17.649
r_dihedral_angle_3_deg16.815
r_lrange_other8.4
r_lrange_it8.399
r_dihedral_angle_1_deg6.468
r_scangle_it5.845
r_scangle_other5.844
r_mcangle_it5.185
r_mcangle_other5.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.582
r_dihedral_angle_4_deg17.649
r_dihedral_angle_3_deg16.815
r_lrange_other8.4
r_lrange_it8.399
r_dihedral_angle_1_deg6.468
r_scangle_it5.845
r_scangle_other5.844
r_mcangle_it5.185
r_mcangle_other5.185
r_scbond_it3.624
r_scbond_other3.624
r_mcbond_it3.362
r_mcbond_other3.362
r_angle_refined_deg1.454
r_angle_other_deg1.18
r_nbd_other0.215
r_nbd_refined0.195
r_symmetry_nbd_other0.183
r_xyhbond_nbd_refined0.175
r_symmetry_nbd_refined0.166
r_symmetry_xyhbond_nbd_refined0.165
r_nbtor_refined0.146
r_symmetry_nbtor_other0.077
r_ncsr_local_group_280.076
r_ncsr_local_group_180.074
r_ncsr_local_group_240.074
r_ncsr_local_group_60.071
r_ncsr_local_group_220.071
r_ncsr_local_group_170.07
r_ncsr_local_group_140.068
r_ncsr_local_group_150.068
r_ncsr_local_group_190.068
r_ncsr_local_group_260.068
r_ncsr_local_group_270.068
r_ncsr_local_group_20.067
r_ncsr_local_group_120.067
r_ncsr_local_group_130.067
r_ncsr_local_group_70.066
r_ncsr_local_group_250.066
r_ncsr_local_group_90.065
r_ncsr_local_group_100.065
r_symmetry_xyhbond_nbd_other0.064
r_ncsr_local_group_40.064
r_ncsr_local_group_230.064
r_ncsr_local_group_50.063
r_ncsr_local_group_110.063
r_ncsr_local_group_160.063
r_chiral_restr0.061
r_ncsr_local_group_10.061
r_ncsr_local_group_210.06
r_ncsr_local_group_80.058
r_ncsr_local_group_30.057
r_ncsr_local_group_200.057
r_metal_ion_refined0.012
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22203
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms208

Software

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