6MC3
Crystal structure of a tetrameric DNA fold-back quadruplex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.4 | 295 | 15% PEG400, 120 mM magnesium chloride, 30 mM sodium cacodylate, equilibrated against 20% PEG400 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 34.135 | α = 90 |
b = 46.43 | β = 90 |
c = 71.894 | γ = 90 |
Symmetry | |
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Space Group | P 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 S 6M | 2017-04-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.92 | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 1.57 | 28.42 | 99.6 | 0.082 | 0.036 | 8.3 | 6.4 | 16520 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.57 | 1.6 | 3.668 | 1.531 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.57 | 28.42 | 15701 | 793 | 99.34 | 0.20272 | 0.20042 | 0.24344 | RANDOM | 37.605 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.77 | -1.22 | 2.99 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 34.314 |
r_sphericity_bonded | 22.41 |
r_long_range_B_refined | 8.322 |
r_long_range_B_other | 7.786 |
r_scangle_other | 7.466 |
r_scbond_it | 6.622 |
r_scbond_other | 6.622 |
r_rigid_bond_restr | 6.003 |
r_angle_refined_deg | 2.086 |
r_angle_other_deg | 1.968 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 744 |
Solvent Atoms | 110 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |