Experiment: 8UQU

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	Protein: 4.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 5% Gly, 2mM GDP, 2mM Magnesium chloride; Screen: Classics II (C6), 0.8M Sodium/Potassium tartrate, 0.1M Bis-Tris pH 8.5, 0.5% (w/v) PEG 5000 MME; Cryo: 20% Glycerole in screen solution.

Crystal Properties
Matthews coefficient	Solvent content
5.14	76.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.971	α = 90
b = 149.971	β = 90
c = 371.921	γ = 120

Symmetry
Space Group	P 65 2 2

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 9M		2021-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9789	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.95	30	100	0.199	0.199	0.05	0.999	16.8	16.5		53143		-3	78.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3	100		0.528	0.593	1.5	17.2

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	2.95	29.91	50134	2699	99.81	0.1791	0.1776	0.2069	RANDOM	78.553

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]
0.79	0.4		0.79		-2.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.536
r_dihedral_angle_4_deg	9.582
r_dihedral_angle_3_deg	9.409
r_dihedral_angle_1_deg	1.617
r_angle_refined_deg	1.375
r_angle_other_deg	0.37
r_chiral_restr	0.068
r_gen_planes_refined	0.054
r_gen_planes_other	0.046
r_bond_refined_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.536
r_dihedral_angle_4_deg	9.582
r_dihedral_angle_3_deg	9.409
r_dihedral_angle_1_deg	1.617
r_angle_refined_deg	1.375
r_angle_other_deg	0.37
r_chiral_restr	0.068
r_gen_planes_refined	0.054
r_gen_planes_other	0.046
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6000
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	137

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.