8KB7

Crystal structure of UDP/mannose-bound AGO61/beta-1,4-N-Acetylglucosaminyltransferase 2 (POMGNT2)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	12% PEG4000, 0.1 M sodium citrate tribasic (pH 6.0), and 0.1 M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
4.05	69.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.019	α = 90
b = 150.002	β = 90
c = 191.481	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 EIGER X 16M		2020-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9000	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.8	50	99.7	0.062	0.999	13.5	3.6		97911

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.97	99.3		0.918	0.569	1.2	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.8	47.92	97911	5042	99.85	0.19304	0.19124	0.22823	RANDOM	88.647

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]
-4.61			6.09		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.411
r_dihedral_angle_4_deg	21.248
r_dihedral_angle_3_deg	19.316
r_long_range_B_refined	15.806
r_long_range_B_other	15.806
r_scangle_other	13.484
r_mcangle_it	11.13
r_mcangle_other	11.13
r_scbond_it	9.221
r_scbond_other	9.22
r_mcbond_it	8.046
r_mcbond_other	8.045
r_dihedral_angle_1_deg	8.007
r_angle_refined_deg	1.634
r_angle_other_deg	1.226
r_chiral_restr	0.071
r_bond_refined_d	0.008
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	16633
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	236

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AutoSol	phasing