6YJR | pdb_00006yjr

Crystal structure of unliganded MGAT5 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V) luminal domain.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M Citrate pH 5.0 16% w/v PEG6000

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.809	α = 90
b = 100.415	β = 90
c = 207.981	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 PILATUS 6M		2018-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.198	48.81	93.4	0.122	0.047	0.998	12.3	7.8		36979

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.49			1.223	0.479	0.615	1.7

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	5zic	2.198	48.81	35113	1866	57.085	0.211	0.2081	0.21	0.2625	0.26	70.676

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]
-2.517			10.152		-7.636

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.424
r_dihedral_angle_4_deg	18.034
r_dihedral_angle_3_deg	17.643
r_lrange_it	7.371
r_lrange_other	7.369
r_dihedral_angle_1_deg	7.238
r_scangle_it	5.548
r_scangle_other	5.547
r_mcangle_it	4.779
r_mcangle_other	4.779
r_scbond_it	3.52
r_scbond_other	3.52
r_mcbond_it	3.181
r_mcbond_other	3.18
r_angle_refined_deg	1.572
r_angle_other_deg	1.246
r_symmetry_xyhbond_nbd_refined	0.311
r_nbd_other	0.232
r_nbd_refined	0.214
r_symmetry_xyhbond_nbd_other	0.208
r_symmetry_nbd_refined	0.198
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.147
r_ncsr_local_group_1	0.089
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7886
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing