2AVH | pdb_00002avh

G4T3G4 dimeric quadruplex structure

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		GGGG(+U)TTGGGG chain A (P21)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	284.15	sodium iodide, sodium cacodylate, PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 284.15K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 29.932	α = 90
b = 37.112	β = 90
c = 43.653	γ = 90

Symmetry
Space Group	C 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	99	CCD	ADSC QUANTUM 4		2004-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9792	ESRF	ID14-4

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	1.5	25	99	0.054			4066	4066

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.54	96.127	98.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	GGGG(+U)TTGGGG chain A (P21)	1.5	23.3	4065	4065	184	98.91	0.199	0.199	0.198	0.1987	0.208	0.2175	RANDOM	19.437

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]
-0.66			0.49		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	1.517
r_angle_refined_deg	1.15
r_scbond_it	1.03
r_symmetry_vdw_refined	0.375
r_nbd_refined	0.31
r_nbtor_refined	0.272
r_symmetry_hbond_refined	0.125
r_xyhbond_nbd_refined	0.11
r_symmetry_metal_ion_refined	0.096
r_metal_ion_refined	0.06
r_chiral_restr	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	233
Solvent Atoms	54
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction