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 | |
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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 | R-Free | 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 | 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 |