8HWI

Bacterial STING from Larkinella arboricola in complex with 3'3'-c-di-GMP

X-RAY DIFFRACTION

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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		277	0.1 M Imidazole pH 7.5, 0.1 M Sodium chloride, 20% v/v Jeffamine ED-2001 pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.987	α = 90
b = 72.489	β = 90
c = 231.066	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		2022-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 07A	0.97625	NSRRC	TPS 07A

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	2.72	30	96.5	0.099	23.3	10.3		30140			45.98

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	2.72	2.82			1.526		8.3

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	2.73	29.31	25497	1343	85.7	0.21172	0.20883	0.26598	RANDOM	57.487

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]
0.06			0.09		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.733
r_dihedral_angle_3_deg	16.791
r_dihedral_angle_4_deg	14.343
r_long_range_B_other	11.236
r_long_range_B_refined	11.235
r_mcangle_it	7.095
r_mcangle_other	7.095
r_scangle_other	6.485
r_dihedral_angle_1_deg	6.053
r_mcbond_it	4.183
r_mcbond_other	4.176
r_scbond_it	3.802
r_scbond_other	3.802
r_angle_other_deg	2.184
r_angle_refined_deg	1.286
r_chiral_restr	0.057
r_bond_other_d	0.033
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
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	8812
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHENIX	phasing
HKL-2000	data reduction