3I5L
Allosteric Modulation of DNA by Small Molecules
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 277.15 | 21% 2-methyl-2,4-pentanediol (MPD), 35 mM calcium acetate, 10 mM Tris pH 7.5 equilibrated in sitting drops against a reservoir of 35% MPD at 4 C. , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 47.01 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 22.5 | α = 66.53 |
b = 25.14 | β = 79.28 |
c = 29.09 | γ = 79.57 |
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 | CCD | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.97 | SSRL | BL12-2 |
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 | 1.175 | 26.472 | 0.124 | 12.5 | 4 | 19011 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.175 | 1.205 | 90.16 | 0.154 | 8.9 | 4 |
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 | AB INITIO PHASING | THROUGHOUT | 1.18 | 26.47 | 16139 | 1835 | 94.55 | 0.103 | 0.09902 | 0.13764 | RANDOM | 5.679 |
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] | |
0.03 | -0.05 | 0.04 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 12.406 |
r_sphericity_bonded | 5.225 |
r_scangle_it | 2.604 |
r_angle_refined_deg | 2.565 |
r_scbond_it | 2.163 |
r_mcangle_it | 2.02 |
r_rigid_bond_restr | 1.725 |
r_mcbond_it | 1.668 |
r_angle_other_deg | 1.481 |
r_mcbond_other | 1.285 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 441 |
Solvent Atoms | 262 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | phasing |