6S24

Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and the peptide 3

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NQA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	Morpheus precipitant mix 4, nitrate phosphate buffer and Morpheus buffer System 1

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.655	α = 90
b = 104.661	β = 90
c = 143.186	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		2018-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	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	2.12	20	94	0.051	0.996	7.7	5.3		41413

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.23	71.9		0.491	0.522	1.2	3.1

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	5NQA	2.12	19.96	39661	1651	93.75	0.19302	0.19119	0.23738	RANDOM	41.609

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]
-1.18			-0.84		2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.209
r_dihedral_angle_4_deg	21.001
r_dihedral_angle_3_deg	17.054
r_long_range_B_refined	8.955
r_long_range_B_other	8.933
r_dihedral_angle_1_deg	7.826
r_scangle_other	6.278
r_mcangle_it	5.675
r_mcangle_other	5.674
r_scbond_it	4.421
r_scbond_other	4.046
r_mcbond_it	3.708
r_mcbond_other	3.706
r_angle_refined_deg	1.688
r_angle_other_deg	1.267
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	4410
Nucleic Acid Atoms	40
Solvent Atoms	201
Heterogen Atoms	105

Software

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