5NDF

Small-molecule inhibition of ppGalNAc-Ts selectively reduces mucin-type O-glycosylation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29610% PEG 8000, 6% ethylene glycol, 100 mM Hepes pH 7
Crystal Properties
Matthews coefficientSolvent content
2.346.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.98α = 90
b = 123.111β = 90
c = 248.152γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim 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
12.3124.0895.50.0510.36.7151903
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.4299.50.5351.66.9

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 REPLACEMENTTHROUGHOUT2FFV2.3124.08147500431695.350.21420.213110.25149RANDOM53.476
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]
-0.04-0.20.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.818
r_dihedral_angle_4_deg19.268
r_dihedral_angle_3_deg17.612
r_long_range_B_other10.725
r_long_range_B_refined10.723
r_scangle_other7.953
r_mcangle_it6.558
r_mcangle_other6.558
r_dihedral_angle_1_deg6.308
r_scbond_it5.196
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.818
r_dihedral_angle_4_deg19.268
r_dihedral_angle_3_deg17.612
r_long_range_B_other10.725
r_long_range_B_refined10.723
r_scangle_other7.953
r_mcangle_it6.558
r_mcangle_other6.558
r_dihedral_angle_1_deg6.308
r_scbond_it5.196
r_scbond_other5.196
r_mcbond_it4.515
r_mcbond_other4.515
r_angle_refined_deg1.729
r_angle_other_deg1.059
r_chiral_restr0.113
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms23778
Nucleic Acid Atoms
Solvent Atoms848
Heterogen Atoms259

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing