5BJO
Crystal structure of the Corn RNA aptamer in complex with DFHO, site-specific 5-iodo-U
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 294 | 30% PEG 550 MME, 0.1 M Tris-HCl pH 8.05 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.94 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 36.269 | ¦Á = 90 |
b = 55.305 | ¦Â = 90 |
c = 99.002 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 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 | CCD | ADSC QUANTUM 315r | 2015-03-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.5498 | ALS | 5.0.2 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.35 | 50 | 99.1 | 32.1 | 11.3 | 7797 |
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 | THROUGHOUT | 2.35 | 49.5 | 7797 | 886 | 98.97 | 0.18448 | 0.17961 | 0.22822 | RANDOM | 52.585 |
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] | |
1.17 | -1.72 | 0.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 9.402 |
r_long_range_B_other | 9.401 |
r_scangle_other | 6.516 |
r_scbond_it | 4.851 |
r_scbond_other | 4.85 |
r_angle_other_deg | 2.339 |
r_angle_refined_deg | 1.905 |
r_chiral_restr | 0.1 |
r_gen_planes_refined | 0.019 |
r_bond_refined_d | 0.009 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 1566 |
Solvent Atoms | 52 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |