7XTL | pdb_00007xtl

Crystal structure of the C-terminal domain of human N-acetylglucosaminyltransferase IVa

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold2 model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M lithium nitrate, 20%(w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
1.82	32.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.699	α = 90
b = 32.49	β = 94.71
c = 85.629	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 S 6M		2022-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	1.97	85.34	100	0.207	0.216	0.06	0.99	8.4	12.8		20101

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	1.97	2.08	100		0.822	0.855	0.234	0.951	2.4	13

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	AlphaFold2 model	1.972	50.579	20082	959	99.945	0.223	0.2204	0.23	0.2663	0.27	61.557

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]
2.945		-0.197	2.991		-5.825

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.939
r_dihedral_angle_3_deg	15.361
r_dihedral_angle_4_deg	13.427
r_dihedral_angle_1_deg	8.117
r_lrange_it	6.605
r_lrange_other	6.601
r_scangle_it	4.735
r_scangle_other	4.733
r_mcangle_other	4.182
r_mcangle_it	4.181
r_scbond_it	3.21
r_scbond_other	3.209
r_mcbond_it	2.969
r_mcbond_other	2.961
r_angle_refined_deg	1.704
r_angle_other_deg	1.265
r_nbd_refined	0.2
r_nbd_other	0.189
r_symmetry_nbd_other	0.182
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.102
r_symmetry_nbd_refined	0.092
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.074
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2331
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms

Software

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