5NT5
The effect of Berenil and Cacodylateon the crystal structure of d(CGTGAATTCACG)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.9 | 290 | 60mM Sodium cacodylate, 17mM MgCl2, 2m M Spermine, 50% MPD, 1.5mM Berenil |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.59 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 25.044 | α = 90 |
b = 41.534 | β = 90 |
c = 64.868 | γ = 90 |
Symmetry | |
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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 | 120 | CCD | AGILENT ATLAS CCD | 2017-04-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION NOVA | 1.54 |
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 | 2.3 | 34.98 | 100 | 4 | 8.6 | 3731 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 1D29 | 2.3 | 34.98 | 3114 | 150 | 99.39 | 0.24765 | 0.24462 | 0.31207 | RANDOM | 31.768 |
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] | |
-0.02 | 0.05 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 6.741 |
r_long_range_B_other | 6.723 |
r_scangle_other | 4.115 |
r_scbond_it | 3.208 |
r_scbond_other | 3.207 |
r_angle_other_deg | 1.832 |
r_angle_refined_deg | 1.733 |
r_chiral_restr | 0.091 |
r_gen_planes_refined | 0.015 |
r_bond_refined_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 486 |
Solvent Atoms | 15 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
SCALA | data scaling |
PHASER | phasing |