7XTM | pdb_00007xtm

Crystal structure of the C-terminal domain of Bombyx mori N-acetylglucosaminyltransferase IV

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	7	293	0.1 M MES-NaOH, pH 7.0, 12%(w/v) PEG20000

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.733	α = 90
b = 64.466	β = 95.092
c = 78.81	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 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	1.47	39.25	96.6	0.052	0.057	0.022	0.999	18.2	6.4		53654

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	1.47	1.55	83		0.526	0.588	0.255	0.841	2.7	5

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	1.47	33.547	53581	2686	96.454	0.226	0.2244	0.23	0.2484	0.25	21.258

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]
-0.6		0.134	-1.848		2.386

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.856
r_dihedral_angle_3_deg	12.794
r_dihedral_angle_4_deg	12.439
r_dihedral_angle_1_deg	8.001
r_lrange_it	4.226
r_lrange_other	4.203
r_scangle_it	1.803
r_scangle_other	1.802
r_angle_refined_deg	1.729
r_angle_other_deg	1.457
r_mcangle_it	1.337
r_mcangle_other	1.337
r_scbond_it	1.151
r_scbond_other	1.151
r_mcbond_it	0.82
r_mcbond_other	0.814
r_nbd_refined	0.203
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.185
r_xyhbond_nbd_refined	0.141
r_nbd_other	0.141
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbd_refined	0.116
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2317
Nucleic Acid Atoms
Solvent Atoms	152
Heterogen Atoms	24

Software

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