9S6A | pdb_00009s6a

Crystal structure of Arabidopsis thaliana FUT11 complexed to GDP and G0

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q9LJK1-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	LiNaK Tris precipitant mix 6 Acetonitrile

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.663	α = 90
b = 41.15	β = 96.89
c = 82.425	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		2024-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.41	20	94.3	0.034	0.999	6.5	2.8		94108

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	1.41	1.49	83.1		0.662

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.41	19.96	90074	3845	93.73	0.20584	0.2049	0.2116	0.22841	0.2373	RANDOM	30.301

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]
-1.93		-0.54	4.5		-2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.199
r_dihedral_angle_2_deg	12.499
r_long_range_B_refined	8.49
r_long_range_B_other	8.414
r_dihedral_angle_1_deg	6.694
r_scangle_other	6.185
r_mcangle_it	4.39
r_mcangle_other	4.389
r_scbond_it	4.058
r_scbond_other	4.058
r_mcbond_it	2.994
r_mcbond_other	2.994
r_angle_refined_deg	1.785
r_angle_other_deg	0.593
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	3280
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	118

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing