Cyclic [G(2',5')pA(3',5')p] is the metazoan second messenger produced by DNA-activated cyclic GMP-AMP synthase.

Gao, P., Ascano, M., Wu, Y., Barchet, W., Gaffney, B.L., Zillinger, T., Serganov, A.A., Liu, Y., Jones, R.A., Hartmann, G., Tuschl, T., Patel, D.J.

doi:10.1016/j.cell.2013.04.046

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X-RAY DIFFRACTION

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4K8V

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Crystallization

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Crystallization Experiments

Method	VAPOR DIFFUSION, HANGING DROP
pH	7.6
Temperature	277.0
Details	0.1 M HEPES, 0.1 M MgAc2, 20% PEG3350, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

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Unit Cell

Length	(Å)	Angle	(°)
a =	86.56	α =	90
b =	84.15	β =	92.74
c =	124.72	γ =	90

Space Group

Diffraction

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Diffraction Experiment

Diffrn ID	1
Data Collection Temperature	200

Diffraction Detector

Detector	CCD
Type	ADSC QUANTUM 315r
Collection Date	2013-01-23

Diffraction Radiation

Monochromator	Si(111)
Diffraction Protocol	SINGLE WAVELENGTH

Diffraction Source

Source	SYNCHROTRON
Type	NSLS BEAMLINE X29A
Wavelength List	0.9790
Site	NSLS
Beamline	X29A

Refinement Data

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Reflection Details

Observed Criterion Sigma (F)	2.0
Observed Criterion Sigma(I)	2.0
Resolution(High)	2
Resolution(Low)	50
Number Reflections(All)	120932
Number Reflections(Observed)	118611
Percent Possible(Observed)	98.08

High Resolution Shell Details

Resolution(High)	2.0
Resolution(Low)	2.07
Percent Possible(All)	98.6

Refinement

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Refinement Statistics

Structure Solution Method	SAD
reflnsShellList	2.0
Resolution(Low)	44.07
Cut-off Sigma(F)	1.35
Number of Reflections(all)	120932
Number of Reflections(Observed)	118611
Number of Reflections(R-Free)	5939
Percent Reflections(Observed)	98.1
R-Factor(Observed)	0.177
R-Work	0.175
R-Free	0.208

Temperature Factor Modeling

Data	Not Available

Resolution Shells

Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	1.9999
Shell Resolution(Low)	2.0226
Number of Reflections(R-Free)	178
Number of Reflections(R-Work)	3112
R-Factor(R-Work)	0.205
R-Factor(R-Free)	0.2499
Percent Reflections(Observed)	82.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.0226
Shell Resolution(Low)	2.0464
Number of Reflections(R-Free)	178
Number of Reflections(R-Work)	3407
R-Factor(R-Work)	0.2003
R-Factor(R-Free)	0.2768
Percent Reflections(Observed)	88.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.0464
Shell Resolution(Low)	2.0713
Number of Reflections(R-Free)	188
Number of Reflections(R-Work)	3526
R-Factor(R-Work)	0.1945
R-Factor(R-Free)	0.2629
Percent Reflections(Observed)	94.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.0713
Shell Resolution(Low)	2.0976
Number of Reflections(R-Free)	186
Number of Reflections(R-Work)	3684
R-Factor(R-Work)	0.1945
R-Factor(R-Free)	0.2242
Percent Reflections(Observed)	96.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.0976
Shell Resolution(Low)	2.1252
Number of Reflections(R-Free)	192
Number of Reflections(R-Work)	3732
R-Factor(R-Work)	0.189
R-Factor(R-Free)	0.2619
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.1252
Shell Resolution(Low)	2.1543
Number of Reflections(R-Free)	210
Number of Reflections(R-Work)	3769
R-Factor(R-Work)	0.1833
R-Factor(R-Free)	0.2426
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.1543
Shell Resolution(Low)	2.1851
Number of Reflections(R-Free)	201
Number of Reflections(R-Work)	3723
R-Factor(R-Work)	0.1783
R-Factor(R-Free)	0.1938
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.1851
Shell Resolution(Low)	2.2177
Number of Reflections(R-Free)	186
Number of Reflections(R-Work)	3797
R-Factor(R-Work)	0.1791
R-Factor(R-Free)	0.2234
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.2177
Shell Resolution(Low)	2.2523
Number of Reflections(R-Free)	201
Number of Reflections(R-Work)	3718
R-Factor(R-Work)	0.1786
R-Factor(R-Free)	0.2293
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.2523
Shell Resolution(Low)	2.2892
Number of Reflections(R-Free)	185
Number of Reflections(R-Work)	3820
R-Factor(R-Work)	0.1776
R-Factor(R-Free)	0.227
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.2892
Shell Resolution(Low)	2.3287
Number of Reflections(R-Free)	208
Number of Reflections(R-Work)	3744
R-Factor(R-Work)	0.1838
R-Factor(R-Free)	0.2292
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.3287
Shell Resolution(Low)	2.3711
Number of Reflections(R-Free)	218
Number of Reflections(R-Work)	3745
R-Factor(R-Work)	0.1813
R-Factor(R-Free)	0.2234
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.3711
Shell Resolution(Low)	2.4167
Number of Reflections(R-Free)	198
Number of Reflections(R-Work)	3822
R-Factor(R-Work)	0.176
R-Factor(R-Free)	0.2304
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.4167
Shell Resolution(Low)	2.466
Number of Reflections(R-Free)	208
Number of Reflections(R-Work)	3805
R-Factor(R-Work)	0.1854
R-Factor(R-Free)	0.2189
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.466
Shell Resolution(Low)	2.5196
Number of Reflections(R-Free)	207
Number of Reflections(R-Work)	3737
R-Factor(R-Work)	0.1863
R-Factor(R-Free)	0.24
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.5196
Shell Resolution(Low)	2.5782
Number of Reflections(R-Free)	183
Number of Reflections(R-Work)	3816
R-Factor(R-Work)	0.1861
R-Factor(R-Free)	0.2251
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.5782
Shell Resolution(Low)	2.6427
Number of Reflections(R-Free)	191
Number of Reflections(R-Work)	3806
R-Factor(R-Work)	0.1893
R-Factor(R-Free)	0.244
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.6427
Shell Resolution(Low)	2.7141
Number of Reflections(R-Free)	197
Number of Reflections(R-Work)	3812
R-Factor(R-Work)	0.1832
R-Factor(R-Free)	0.2147
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.7141
Shell Resolution(Low)	2.794
Number of Reflections(R-Free)	209
Number of Reflections(R-Work)	3813
R-Factor(R-Work)	0.1845
R-Factor(R-Free)	0.2017
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.794
Shell Resolution(Low)	2.8841
Number of Reflections(R-Free)	183
Number of Reflections(R-Work)	3807
R-Factor(R-Work)	0.1838
R-Factor(R-Free)	0.2056
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.8841
Shell Resolution(Low)	2.9872
Number of Reflections(R-Free)	225
Number of Reflections(R-Work)	3779
R-Factor(R-Work)	0.1834
R-Factor(R-Free)	0.2322
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.9872
Shell Resolution(Low)	3.1068
Number of Reflections(R-Free)	195
Number of Reflections(R-Work)	3837
R-Factor(R-Work)	0.1788
R-Factor(R-Free)	0.2262
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.1068
Shell Resolution(Low)	3.2481
Number of Reflections(R-Free)	199
Number of Reflections(R-Work)	3815
R-Factor(R-Work)	0.1845
R-Factor(R-Free)	0.2284
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.2481
Shell Resolution(Low)	3.4193
Number of Reflections(R-Free)	205
Number of Reflections(R-Work)	3810
R-Factor(R-Work)	0.1722
R-Factor(R-Free)	0.2243
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.4193
Shell Resolution(Low)	3.6334
Number of Reflections(R-Free)	214
Number of Reflections(R-Work)	3828
R-Factor(R-Work)	0.1666
R-Factor(R-Free)	0.1858
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.6334
Shell Resolution(Low)	3.9138
Number of Reflections(R-Free)	187
Number of Reflections(R-Work)	3842
R-Factor(R-Work)	0.1554
R-Factor(R-Free)	0.1799
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.9138
Shell Resolution(Low)	4.3074
Number of Reflections(R-Free)	234
Number of Reflections(R-Work)	3850
R-Factor(R-Work)	0.1542
R-Factor(R-Free)	0.1649
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	4.3074
Shell Resolution(Low)	4.93
Number of Reflections(R-Free)	175
Number of Reflections(R-Work)	3857
R-Factor(R-Work)	0.1476
R-Factor(R-Free)	0.1651
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	4.93
Shell Resolution(Low)	6.2085
Number of Reflections(R-Free)	205
Number of Reflections(R-Work)	3900
R-Factor(R-Work)	0.1799
R-Factor(R-Free)	0.2036
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	6.2085
Shell Resolution(Low)	44.077
Number of Reflections(R-Free)	193
Number of Reflections(R-Work)	3959
R-Factor(R-Work)	0.1814
R-Factor(R-Free)	0.186
Percent Reflections(Observed)	99.0

RMS Deviations

Parameter Type	Deviation from Ideal
f_plane_restr	0.005
f_chiral_restr	0.085
f_dihedral_angle_d	16.047
f_angle_d	1.207
f_bond_d	0.01

Number of Non-Hydrogen Atoms Used in Refinement

Protein Atoms	11957
Nucleic Acid Atoms	0
Heterogen Atoms	4
Solvent Atoms	1357

Software and Computing

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Computing

Data Collection	CBASS
Data Reduction (intensity integration)	HKL-2000
Data Reduction (data scaling)	HKL-2000
Structure Solution	SOLVE
Structure Refinement	PHENIX (PHENIX.REFINE: 1.8.2_1309)

Software

refinement	PHENIX version: (phenix.refine: 1.8.2_1309)
model building	SOLVE
data collection	CBASS

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