6FWZ

Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) in complex with UDP-GlcNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5LEV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP92930.1M bicine pH 9.0 -- 0.05M sodium chloride -- 37.5% PEG300
Crystal Properties
Matthews coefficientSolvent content
3.9168.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.459α = 90
b = 102.459β = 90
c = 238.209γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-01-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
13.159.551000.0950.1010.0330.99914.49.51419785.75
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.181002.3762.5050.7840.3871.19.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5LEV3.1301339572899.780.223270.222570.23624RANDOM128.475
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]
0.240.120.24-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.766
r_dihedral_angle_4_deg16.324
r_dihedral_angle_3_deg15.474
r_long_range_B_other9.148
r_long_range_B_refined9.147
r_scangle_other5.629
r_mcangle_it4.669
r_mcangle_other4.668
r_dihedral_angle_1_deg3.884
r_scbond_it3.599
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.766
r_dihedral_angle_4_deg16.324
r_dihedral_angle_3_deg15.474
r_long_range_B_other9.148
r_long_range_B_refined9.147
r_scangle_other5.629
r_mcangle_it4.669
r_mcangle_other4.668
r_dihedral_angle_1_deg3.884
r_scbond_it3.599
r_scbond_other3.599
r_mcbond_it2.968
r_mcbond_other2.968
r_angle_refined_deg1.554
r_angle_other_deg1.018
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2892
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing