3QSC | pdb_00003qsc

The first crystal structure of a human telomeric G-quadruplex DNA bound to a metal-containing ligand (a copper complex)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1K8P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	Initial conditions were 0.6 mM quadruplex DNA, 0.6 mM ligand, 0.4% PEG 2000 (w/v), 100mM potassium chloride, 100mM sodium chloride, 100mM lithium sulphate, 20mM potassium cacodylate, equilibrated against a reservoir well solution of 60% PEG 2000 (w/v), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.753	α = 90
b = 54.786	β = 90
c = 33.43	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	105	CCD	ADSC QUANTUM 315r		2010-10-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.90740, 0.92060, 0.92110	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.254	21.188	98.2	0.034	24.9	3.8	2020	2020

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.38	91.5		0.095	0.095	8.1	2.6	271

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1K8P	2.4	15	1687	1687	77	99.06	0.2142	0.2132	0.22	0.2343	0.25	RANDOM	35.2997

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]
-0.25			0.84		-0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	4.31
r_scbond_it	2.847
r_angle_refined_deg	1.559
r_chiral_restr	0.056
r_gen_planes_refined	0.023
r_bond_refined_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	231
Solvent Atoms	27
Heterogen Atoms	48

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
SHELXD	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.