8HY9

Bacterial STING from Riemerella anatipestifer 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
experimental model	PDB	7EBD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1 M Tris pH 8.5, 0.2 M calcium chloride dihydrate, 40 % v/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.51	α = 90
b = 40.99	β = 105.041
c = 36.196	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER X 16M		2022-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 07A	0.97624	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	1.46	30	99.3	0.054	30.227	6.2		24248

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	1.46	1.51	95		0.489	2.92	4.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7EBD	1.462	22.805	24109	1219	98.328	0.183	0.1813	0.2095	17.222

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]
0.204		0.018	-0.23		0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.234
r_dihedral_angle_4_deg	19.3
r_dihedral_angle_3_deg	12.417
r_dihedral_angle_1_deg	6.728
r_lrange_it	5.786
r_lrange_other	5.736
r_scangle_it	4.475
r_scangle_other	4.473
r_scbond_other	2.958
r_scbond_it	2.954
r_mcangle_other	2.703
r_mcangle_it	2.701
r_mcbond_it	1.768
r_mcbond_other	1.76
r_angle_refined_deg	1.437
r_angle_other_deg	1.37
r_nbd_refined	0.227
r_nbd_other	0.181
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.176
r_symmetry_xyhbond_nbd_refined	0.174
r_xyhbond_nbd_refined	0.164
r_symmetry_nbd_refined	0.162
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.074
r_metal_ion_refined	0.066
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1286
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	47

Software

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