3CE5 | pdb_00003ce5

A bimolecular parallel-stranded human telomeric quadruplex in complex with a 3,6,9-trisubstituted acridine molecule BRACO19

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	285.15	1.6 mM DNA, 1.6 mM BRACO19, 200 mM ammonium sulphate, 20 mM sodium chloride, 20 mM potassium chloride, 20 mM lithium sulphate and 36 mM potassium cacodylate buffer at pH 6.5 equilibrated against 1.6 M ammonium sulphate , VAPOR DIFFUSION, HANGING DROP, temperature 285.15K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.338	α = 90
b = 70.338	β = 90
c = 34.293	γ = 90

Symmetry
Space Group	I 4

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2008-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	35.17	99.7	0.065	9.8	2.9	3003	2994		3	58.2

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	2.5	2.59	100		0.31	2.4	2.8	291

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	PDB Entry 1K8P	2.5	35.17	2992	2852	140	100	0.18446	0.18446	0.18298	0.18	0.21341	0.22	RANDOM	23.482

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]
2.08			2.08		-4.15

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	3.864
r_scbond_it	2.845
r_angle_refined_deg	2.813
r_nbtor_refined	0.342
r_nbd_refined	0.306
r_xyhbond_nbd_refined	0.207
r_symmetry_hbond_refined	0.196
r_symmetry_vdw_refined	0.193
r_metal_ion_refined	0.162
r_chiral_restr	0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	3.864
r_scbond_it	2.845
r_angle_refined_deg	2.813
r_nbtor_refined	0.342
r_nbd_refined	0.306
r_xyhbond_nbd_refined	0.207
r_symmetry_hbond_refined	0.196
r_symmetry_vdw_refined	0.193
r_metal_ion_refined	0.162
r_chiral_restr	0.115
r_bond_refined_d	0.024
r_gen_planes_refined	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	502
Solvent Atoms	54
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
PHASER	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.