4R4D
Racemic crystal structure of a magnesium-bound B-DNA duplex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 1 mM DNA, 50 mM sodium cacodylate, 200 mM magnesium chloride, 2.5 mM spermine, 30% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.79 | 31.17 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.61 | α = 70.76 |
b = 32.951 | β = 80.77 |
c = 46.25 | γ = 73.77 |
Symmetry | |
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Space Group | P -1 |
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 PILATUS 6M | 2014-06-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.9998 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.29 | 43.54 | 91.4 | 0.023 | 14.11 | 1.9 | 42395 | 38749 | 2 | 2 | 47.68 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.29 | 1.37 | 86.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | PDB ENTRY 3R86 | 1.29 | 43.54 | 40186 | 37851 | 1979 | 94.19 | 0.2709 | 0.2689 | 0.3113 | RANDOM | 18.519 |
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] | |
0.25 | 0.2 | -0.03 | -0.54 | 0.16 | 0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 14.304 |
r_sphericity_bonded | 10.356 |
r_rigid_bond_restr | 9.989 |
r_angle_refined_deg | 2.298 |
r_chiral_restr | 0.121 |
r_gen_planes_refined | 0.028 |
r_bond_refined_d | 0.013 |
r_bond_other_d | |
r_angle_other_deg | |
r_dihedral_angle_1_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 808 |
Solvent Atoms | 134 |
Heterogen Atoms | 9 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
d*TREK | data scaling |