7XTN

Crystal structure of the C-terminal domain of Bombyx mori N-acetylglucosaminyltransferase IV in complex with N-acetylglucosamine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1 M MES-NaOH, pH 7.0, 12%(w/v) PEG20000, 10 mM N-acetylglucosamine

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.697	α = 90
b = 64.098	β = 95.891
c = 79.148	γ = 90

Symmetry
Space Group	P 1 21 1

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 2M		2021-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.15	39.37	98.6	0.046	0.05	0.019	0.999	18.1	6.7		113597

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)	Redundancy	Number Unique Reflections (All)
1	1.15	1.21	94.9		0.81	0.879	0.336	0.782	2.3	6.6

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AlphaFold2 model	1.15	32.545	113579	5719	98.625	0.194	0.1933	0.2087	18.769

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]
0.534		-0.401	0.215		-0.653

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.022
r_dihedral_angle_4_deg	18.822
r_dihedral_angle_3_deg	12.612
r_dihedral_angle_1_deg	7.733
r_lrange_it	4.199
r_lrange_other	4.096
r_scangle_it	1.998
r_scangle_other	1.998
r_angle_refined_deg	1.677
r_angle_other_deg	1.423
r_mcangle_it	1.317
r_mcangle_other	1.317
r_scbond_it	1.264
r_scbond_other	1.263
r_mcbond_it	0.811
r_mcbond_other	0.81
r_symmetry_nbd_refined	0.239
r_nbd_other	0.209
r_nbd_refined	0.2
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.143
r_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2494
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building