4WNH

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Xylose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.2 M Li2SO4, 0.1 M Bis-Tris, pH 6.5, and 21% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.481	α = 90
b = 89.481	β = 90
c = 42.895	γ = 120

Symmetry
Space Group	P 3

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		2014-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1000	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	50	100	0.07	19.5	5.7		28026

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	100		0.651	2.3	5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.95	50	26616	1408	99.99	0.19429	0.1927	0.22448	RANDOM	33.55

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]
-0.03	-0.02		-0.03		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.196
r_dihedral_angle_4_deg	18.458
r_dihedral_angle_3_deg	15.408
r_dihedral_angle_1_deg	5.69
r_long_range_B_refined	5.133
r_long_range_B_other	5.126
r_scangle_other	3.36
r_mcangle_other	2.983
r_mcangle_it	2.982
r_scbond_it	2.027
r_scbond_other	2.026
r_mcbond_it	1.837
r_mcbond_other	1.824
r_angle_refined_deg	1.278
r_angle_other_deg	0.83
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2698
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	55

Software

Software
Software Name	Purpose
REFMAC	refinement