2QS6

Structure of a Hoogsteen antiparallel duplex with extra-helical thymines

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RSB	D(ATATAT)2 model with Hoogsteen base pairs (from NDB entry UD0049)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	Drop: 1.0mM octamer, 10% MPD, 22mM sodium cacodylate, 10mM magnesium chloride, 1.5mM spermine tetrachloride. Reservoir: from 25% to 45% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.836	α = 90
b = 39.54	β = 95.08
c = 71.753	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113.15	CCD	MAR CCD 165 mm		2004-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM16	0.9790	ESRF	BM16

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	3.08	71.43	98	0.077	13.5	5.35	6262	6262		-3

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	3.08	3.21	94.2		0.222	3.6

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	D(ATATAT)2 model with Hoogsteen base pairs (from NDB entry UD0049)	3.08	71.43	6503	5188	555	88.86	0.21446	0.20689	0.21	0.2895	0.31	RANDOM	65.775

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]
0.96		-4.62	-1.18		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	1.668
r_scbond_it	1.184
r_angle_refined_deg	1.07
r_angle_other_deg	0.939
r_xyhbond_nbd_refined	0.404
r_symmetry_vdw_other	0.29
r_nbtor_refined	0.25
r_symmetry_vdw_refined	0.234
r_symmetry_hbond_refined	0.19
r_xyhbond_nbd_other	0.112
r_bond_refined_d	0.085
r_chiral_restr	0.061
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_other
r_metal_ion_refined
r_metal_ion_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	2181
Solvent Atoms	40
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing