3SKT
Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.05 M Na-HEPES, pH 7.5, ~40 % (v/v) pentaerythritol propoxylate, 0.2 M KCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.86 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 97.031 | ¦Á = 90 |
b = 34.632 | ¦Â = 92.81 |
c = 111.598 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 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 | ADSC QUANTUM 315 | 2010-04-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | 1.5 | NSLS | X29A |
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 | 3.1 | 20 | 97.9 | 0.136 | 19.9 | 5.9 | 7069 | 6921 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.1 | 3.21 | 85.2 | 0.24 | 6.6 | 4.5 | 586 |
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 | Molrep | THROUGHOUT | 3.1 | 20 | 6532 | 317 | 98.12 | 0.19867 | 0.19607 | 0.252 | RANDOM | 64.159 |
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] | |
-4.68 | -7.95 | -3.66 | 7.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 1.186 |
r_angle_refined_deg | 1.132 |
r_scbond_it | 0.702 |
r_nbtor_refined | 0.283 |
r_nbd_refined | 0.186 |
r_symmetry_hbond_refined | 0.173 |
r_xyhbond_nbd_refined | 0.171 |
r_symmetry_vdw_refined | 0.141 |
r_chiral_restr | 0.057 |
r_bond_refined_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 2826 |
Solvent Atoms | 10 |
Heterogen Atoms | 57 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |