Experiment: 1ILC

DNA Bending by an Adenine-Thymine Tract and Its Role in Gene Regulation.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		standard B-DNA fiber coordinates

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	MPD, magnesium chloride, spermine.4HCl, Na cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

Crystal Properties
Matthews coefficient	Solvent content
2.29	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.821	α = 74.42
b = 40.16	β = 76.44
c = 39.46	γ = 59.9

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IIC	Yale-type mirrors	1997-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-C	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	19	95.7	0.051	0.051	25.8	3.7	9810	9810

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)
	2.2	2.24	95		0.654	0.654	2	3.6	491

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Fiber model of B-DNA	2.2	19	9810	8475	456	86.4	0.224	0.222	0.2414	0.292	random	30.1

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	17.7
x_angle_deg	1.6
x_bond_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1458
Solvent Atoms	114
Heterogen Atoms

Software

Software
Software Name	Purpose
MFT	model building
ULTIMA	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
MFT	phasing
ULTIMA	phasing