1S47 | pdb_00001s47

Crystal structure analysis of the DNA quadruplex d(TGGGGT)S2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S45	PDB ENTRY 1S45

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	277	PEG 400, sodium cacodylate, magnesium chloride, spermine, tetrahydrochlorhide, thallium acetate, lysine-anthraquinone, d(TGGGGT), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.50

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.319	α = 90
b = 56.341	β = 99.17
c = 51.746	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD				M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.5	20		0.08		5.43		10915			6.4

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)
	2.5	2.59	97.3		0.16

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1S45	2.5	19.84	2	10915	4281	446	79	0.224	0.224	0.26	0.311	RANDOM	20.1

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]
-13.16		2.95	15.31		-2.16

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.7
c_mcangle_it	2.43
c_mcbond_it	1.71
c_improper_angle_d	1.09
c_angle_deg	0.7
c_bond_d	0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1432
Solvent Atoms	86
Heterogen Atoms	13

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing