Experiment: 3UBI

The Absence of Tertiary Interactions in a Self-Assembled DNA Crystal Structure

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	CRYSTALLIZATION CONDITIONS: GROWN BY VAPOR DIFFUSION WHILE TREATED WITH A CONTROLLED TEMPERATURE GRADIENT FROM 333 DEGS TO 293 DEGS., PH 8.5, VAPOR DIFFUSION, SITTING DROP

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 169.98	α = 90
b = 169.98	β = 90
c = 88.638	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	190	CCD	ADSC QUANTUM 315r	GRAPHITE		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.1	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	6.805	49.069	100			1413	1413

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	6.8046	49.069	0.24	1413	141	86.85	0.1401	0.1385	0.152	0.2004	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]
67.1315			67.1315		811.9265

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	30.989
f_angle_d	0.814
f_chiral_restr	0.036
f_bond_d	0.003
f_plane_restr	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1265
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing