1N7A
RIP-Radiation-damage Induced Phasing
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 1 mM (single strand) RNA, 20 mM sodium cacodylate buffer, pH 6.0, 5 mM spermine tetrachloride, 32 mM KCl and 2 % (v/v) methyl-2,4-pentanediol (MPD) against 25 % MPD in the reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.77 | 30.36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 31.233 | α = 90 |
b = 51.102 | β = 90 |
c = 70.651 | γ = 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 4 | 2002-02-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | 0.933 | ESRF | ID14-2 |
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 | 1.2 | 20 | 99.5 | 0.087 | 10.83 | 4.24 | 35974 | 35974 | -3 | 4.9 |
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) | |||||||||||
1.2 | 1.27 | 98.5 | 0.341 | 3.82 | 4.19 | 5469 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | THROUGHOUT | 1.2 | 20 | 35974 | 35974 | 1802 | 99.71 | 0.12533 | 0.12533 | 0.12369 | 0.15626 | RANDOM | 9.356 |
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] | |
0.02 | 0.2 | -0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_bonded | 4.684 |
r_sphericity_free | 2.853 |
r_scangle_it | 2.79 |
r_scbond_it | 2.12 |
r_angle_refined_deg | 1.533 |
r_rigid_bond_restr | 1.164 |
r_nbd_refined | 0.374 |
r_symmetry_hbond_refined | 0.144 |
r_symmetry_vdw_refined | 0.133 |
r_xyhbond_nbd_refined | 0.081 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 1024 |
Solvent Atoms | 181 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
ProDC | data collection |
XDS | data reduction |
SHELXD | phasing |
SHARP | phasing |
REFMAC | refinement |
XDS | data scaling |