Experiment: 2DEV

Crystal structure of tt0972 protein from Thermus Thermophilus with Cs(+) ions

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DEH	PDB ENTRY 2DEH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	6% PEG 4000, 60mM sodium acetate, 60mM lithium chloride, 100mM cesium chloride, 0.5mM nickel chloride, 30mM TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.764	α = 90
b = 65.764	β = 90
c = 204.285	γ = 90

Symmetry
Space Group	P 41 21 2

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	RIGAKU JUPITER 210	mirrors	2004-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	0.97910	SPring-8	BL26B2

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	2.45	20	98.8	0.043	34.9	6.9	17359	17151		-3	35.8

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	2.45	2.54	97.1		0.499	3.4	6.1	1626

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2DEH	2.45	19.89	17151	16631	805	96.3	0.248	0.246	0.246	0.2462	0.288	0.2871	RANDOM	55.8

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]
2.88			2.88		-5.76

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.9
c_angle_deg	1.4
c_improper_angle_d	0.67
c_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3196
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	4

Software

Software
Software Name	Purpose
CNS	refinement
BSS	data collection
SCALEPACK	data scaling
CNS	phasing