7XJV | pdb_00007xjv

Crystal Structure of Alpha-1,3-mannosyltransferase MNT2 from Saccharomyces cerevisiae, Mn/GDP-mannose form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		Predicted structure model by Alphafold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	PEG 20000

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.849	α = 90
b = 131.189	β = 90
c = 169.552	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		2022-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	0.988	7.7	6.9		139005

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.97			0.947

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	Predicted structure model by Alphafold	2.8	40.003	72434	3516	99.916	0.215	0.2135	0.22	0.2508	0.25	71.951

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]
2.681			3.125		-5.807

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.078
r_dihedral_angle_3_deg	13.45
r_dihedral_angle_4_deg	9.609
r_lrange_it	7.224
r_lrange_other	7.224
r_dihedral_angle_1_deg	5.745
r_scangle_it	4.616
r_scangle_other	4.615
r_mcangle_it	4.566
r_mcangle_other	4.566
r_scbond_it	2.81
r_scbond_other	2.81
r_mcbond_it	2.765
r_mcbond_other	2.765
r_angle_refined_deg	1.204
r_angle_other_deg	1.061
r_nbd_other	0.208
r_nbd_refined	0.171
r_symmetry_nbd_other	0.162
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.156
r_xyhbond_nbd_refined	0.137
r_ncsr_local_group_6	0.101
r_ncsr_local_group_4	0.096
r_ncsr_local_group_5	0.094
r_ncsr_local_group_3	0.093
r_symmetry_xyhbond_nbd_refined	0.089
r_ncsr_local_group_2	0.089
r_ncsr_local_group_1	0.087
r_symmetry_nbtor_other	0.071
r_symmetry_xyhbond_nbd_other	0.07
r_chiral_restr	0.04
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16882
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms	267

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing