3EUM | pdb_00003eum

A bimolecular anti-parallel-stranded Oxytricha nova telomeric quadruplex in complex with a 3,6-disubstituted acridine BSU-6066

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L1H	PDB ID 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
2.09	41.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.62	α = 90
b = 42.307	β = 90
c = 27.079	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	CCD	OXFORD ONYX CCD	Oxford diffraction Nova	2007-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	1.540562

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	1.78	24.35	81.7	0.079	15.57	2.3	6576	5372			14.2

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)
	1.78	1.93	39.1		0.28		1.3	539

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 1L1H	1.78	24.35	5372	5106	238	81.91	0.2241	0.22174	0.23	0.27042	0.29	RANDOM	16.544

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]
-0.87			-0.93		1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	2.055
r_angle_refined_deg	1.894
r_scbond_it	1.438
r_nbd_refined	0.34
r_nbtor_refined	0.294
r_symmetry_hbond_refined	0.272
r_symmetry_vdw_refined	0.153
r_xyhbond_nbd_refined	0.123
r_metal_ion_refined	0.082
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	506
Solvent Atoms	52
Heterogen Atoms	42

Software

Software
Software Name	Purpose
CrysalisPro	data collection
PHASER	phasing
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling