8HWJ | pdb_00008hwj

Bacterial STING from Epilithonimonas lactis in complex with 3'3'-c-di-AMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1 M MES pH 6.0, 0.1 M Sodium chloride, 30 % v/v PEG 3500

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.171	α = 90
b = 52.713	β = 114.883
c = 88.932	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		2022-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 07A	0.97626	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	2.55	30	96.5	0.121	14.1	6.3		20886

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	2.55	2.64			0.578	2.3	5.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.553	25.769	19584	962	89.818	0.197	0.195	0.2	0.2276	0.23	45.432

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]
0.439		0.571	-0.735		-0.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.829
r_dihedral_angle_3_deg	18.753
r_dihedral_angle_4_deg	18.662
r_lrange_other	10.578
r_lrange_it	10.577
r_dihedral_angle_1_deg	6.597
r_mcangle_it	6.585
r_mcangle_other	6.584
r_scangle_it	6.455
r_scangle_other	6.452
r_mcbond_it	3.972
r_mcbond_other	3.972
r_scbond_it	3.881
r_scbond_other	3.878
r_angle_other_deg	2.272
r_angle_refined_deg	1.438
r_nbd_other	0.288
r_symmetry_nbd_other	0.231
r_symmetry_nbd_refined	0.217
r_nbd_refined	0.209
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.146
r_symmetry_xyhbond_nbd_other	0.124
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.072
r_bond_other_d	0.034
r_bond_refined_d	0.008
r_gen_planes_other	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5151
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	88

Software

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