5NDF

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FFV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		296	10% PEG 8000, 6% ethylene glycol, 100 mM Hepes pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.45

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2016-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	124.08	95.5	0.05	10.3	6.7		151903

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	99.5		0.535	1.6	6.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2FFV	2.3	124.08	147500	4316	95.35	0.2142	0.21311	0.25149	RANDOM	53.476

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			-0.2		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.818
r_dihedral_angle_4_deg	19.268
r_dihedral_angle_3_deg	17.612
r_long_range_B_other	10.725
r_long_range_B_refined	10.723
r_scangle_other	7.953
r_mcangle_it	6.558
r_mcangle_other	6.558
r_dihedral_angle_1_deg	6.308
r_scbond_it	5.196
r_scbond_other	5.196
r_mcbond_it	4.515
r_mcbond_other	4.515
r_angle_refined_deg	1.729
r_angle_other_deg	1.059
r_chiral_restr	0.113
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
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 Atoms	Number
Protein Atoms	23778
Nucleic Acid Atoms
Solvent Atoms	848
Heterogen Atoms	259

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing