5EW4
Crystal structure of C9ORF72 Antisense CCCCGG repeat RNA associated with Lou Gehrig's disease and frontotemporal dementia, crystallized with Sr2+
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 0.04 M sodium cacodylate, 50 mM KCl, 0.04 M LiCl, 0.012 M spermine, 0.08 M strontium chloride, 10% (v/v) (+/-)-2-methyl-2,4-pentanediol, equilibrated against 35% (v/v) (+/-)-2-methyl-2,4-pentanediol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.02 | α = 90 |
b = 47.615 | β = 90 |
c = 58.9 | 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 315r | monochromator | 2014-04-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97924 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.47 | 50 | 98.6 | 0.032 | 0.036 | 0.016 | 14.1 | 4.5 | 20000 | 13.58 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.47 | 1.5 | 89.4 | 0.542 | 0.648 | 0.343 | 0.713 | 2.9 | 888 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | 1.47 | 23.923 | 1.38 | 19269 | 1928 | 95.32 | 0.2179 | 0.2155 | 0.2389 | throughout | 23.1584 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 6.489 |
f_angle_d | 0.508 |
f_chiral_restr | 0.025 |
f_bond_d | 0.024 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 818 |
Solvent Atoms | 162 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-3000 | data scaling |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
ACORN | phasing |