7OBJ | pdb_00007obj

Carbon regulatory PII-like protein SbtB from Synechocystis sp. 6803 in complex with cyclic di-AMP (c-di-AMP)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O3R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		294	0.1M phosphate-citrate pH 4.2, 40% (w/v) PEG 300

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.171	α = 90
b = 63.171	β = 90
c = 81.733	γ = 120

Symmetry
Space Group	P 32

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 PILATUS 6M-F		2016-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	32.74	99.7	0.064	1	20.61	10.3		24685

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.12			2.231	0.43	1.03	10.1

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5O3R	2	32.74	23454	1231	99.64	0.1797	0.1779	0.215	0.2147	RANDOM	57.982

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]
0.41	0.21		0.41		-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.037
r_dihedral_angle_4_deg	25.179
r_dihedral_angle_3_deg	14.631
r_dihedral_angle_1_deg	6.561
r_angle_refined_deg	1.927
r_angle_other_deg	1.32
r_chiral_restr	0.103
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.008
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2287
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling