3ES0 | pdb_00003es0

A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6048

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L1H	PDB entry 1L1H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	285.15	2 microliter drops containing 5% v/v MPD, 0.50 mM DNA, 0.25 mM Ligand, 40 mM Potassium chloride, 5 mM Magnesium chloride, 4.1 Spermine equilibrated against 35% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285.15K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.525	α = 90
b = 42.462	β = 90
c = 27.299	γ = 90

Symmetry
Space Group	P 21 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	105	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2006-11-02	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	2.2	24.5	99.7	0.041	18.1	2.91	3561	3549		3	27.135

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)
	2.2	2.28	100		0.085	10.2	2.93	348

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1L1H	2.2	24.5	3549	160	99.63	0.19682	0.19452	0.19	0.24507	0.25	RANDOM	11.105

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]
-0.18			-0.98		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.726
r_scangle_it	1.361
r_scbond_it	0.902
r_nbd_refined	0.342
r_nbtor_refined	0.287
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.136
r_metal_ion_refined	0.091
r_chiral_restr	0.053

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.726
r_scangle_it	1.361
r_scbond_it	0.902
r_nbd_refined	0.342
r_nbtor_refined	0.287
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.139
r_symmetry_hbond_refined	0.136
r_metal_ion_refined	0.091
r_chiral_restr	0.053
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	506
Solvent Atoms	56
Heterogen Atoms	42

Software

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

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.