7C0F

Crystal structure of a dinucleotide-binding protein of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form I)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.2M ammonium phosphate, 0.1M sodium cacodylate pH 6.5, 30% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.16	α = 90
b = 120.88	β = 90
c = 66.06	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	IMAGE PLATE	RIGAKU RAXIS IV++	VariMax HF	2017-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.15	66.06	98.2	0.105	0.148	0.104	0.987	6.9	2.8		48571

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	95.1		0.429	0.594	0.41	0.697	2.5	2.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4MFI	2.15	66.06	46107	2429	97.91	0.1604	0.1582	0.2041	RANDOM	23.322

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]
-6.44		0.66	6.57		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.894
r_dihedral_angle_4_deg	18.788
r_dihedral_angle_3_deg	16.725
r_dihedral_angle_1_deg	6.475
r_angle_refined_deg	1.927
r_angle_other_deg	1.468
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.894
r_dihedral_angle_4_deg	18.788
r_dihedral_angle_3_deg	16.725
r_dihedral_angle_1_deg	6.475
r_angle_refined_deg	1.927
r_angle_other_deg	1.468
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6084
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	255

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM133198.