7JJF
Sarcin-ricin loop with modified residue.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291 | RNA was dissolved in 1 mM Na2 EDTA (pH 8.0) and 10 mM Tris-HCl (pH 8.0) to attain 350 uM final RNA concentration. The RNA sample was annealed by heating at 65 C for 2 min and slowly cooling to room temperature. Crystallization set-ups were made by mixing 4 uL of RNA solution with 2 uL of a crystallization buffer composed of 3.0 M ammonium sulfate, 10 mM magnesium chloride, 10 mM manganese chloride, and 50 mM potassium 3-(N-morpholino) propanesulfonic acid (MOPS), pH 7.0 at 18 C. Crystals appear in about two weeks time. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.81 | 32.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 29.34 | α = 90 |
b = 29.34 | β = 90 |
c = 75.661 | γ = 90 |
Symmetry | |
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Space Group | P 43 |
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 | PIXEL | Bruker PHOTON III | 2020-03-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | LIQUID ANODE | Excillum MetalJet D2+ 70 kV | 1.3418 |
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 | 27.36 | 94.1 | 0.089 | 23.47 | 17 | 4.79 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.2 | 1.24 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3DVZ | 1.2 | 27.36 | 4.58 | 36363 | 3874 | 92.1 | 0.184 | 0.177 | 0.214 | 10.76 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.367 |
f_angle_d | 1.342 |
f_chiral_restr | 0.054 |
f_plane_restr | 0.009 |
f_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 578 |
Solvent Atoms | 103 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PROTEUM PLUS | data reduction |
PROTEUM PLUS | data scaling |
PHASER | phasing |