3H3Z

Crystal structure of a putative cyclic nucleotide binding protein (spoa0323) from ruegeria pomeroyi dss-3 at 2.35 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	1.2600M (NH4)2SO4, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.052	α = 90
b = 137.052	β = 90
c = 94.937	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-01-19	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2008-10-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2
2	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97967,0.94645	APS	23-ID-B

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	2.35	28.724	98.2	0.047	11.09	3.82		27604		-3	56.796

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)
	2.35	2.43	96		0.603	1.4

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	MAD	THROUGHOUT	2.35	28.724	27596	1409	99.83	0.204	0.202	0.236	RANDOM	71.309

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]
-0.62	-0.31		-0.62		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.134
r_dihedral_angle_4_deg	15.271
r_dihedral_angle_3_deg	12.223
r_scangle_it	8.009
r_scbond_it	6.013
r_dihedral_angle_1_deg	3.534
r_mcangle_it	3.417
r_mcbond_it	2.094
r_angle_refined_deg	1.725
r_angle_other_deg	1.055
r_mcbond_other	0.685
r_symmetry_vdw_other	0.317
r_nbd_refined	0.214
r_nbtor_refined	0.18
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.158
r_symmetry_vdw_refined	0.135
r_nbtor_other	0.094
r_chiral_restr	0.064
r_bond_refined_d	0.018
r_xyhbond_nbd_other	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3391
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing