Experiment: 2FII

Crystal Structure Analysis of the B-DNA Dodecamer CGCGAAT-aU-CGCG, with Incorporated Arabino-Uridin (aU)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	355D	NDB entry BDL084/PDB entry 355D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	291	Final droplet composition: 0.6 mM oligonucleotide, 20mM sodium cacodylate, 6.3 mM Mg(OAc)2, and 3 mM spermine tetrahydrochloride., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.699	α = 90
b = 39.915	β = 90
c = 65.564	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103	CCD	MARRESEARCH		2002-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B		APS	5ID-B

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	1.24	30	99.8	0.077				19780

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	1.24	1.34	99.5		0.168

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	NDB entry BDL084/PDB entry 355D	1.24	30	19728	985		0.158	0.155		0.1582	0.212	0.1937	RANDOM

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	486
Solvent Atoms	131
Heterogen Atoms	1

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
SHELXL-97	refinement
CNS	phasing