7MKT
Crystal structure of r(GU)11G-NMM complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | The RNA smaple was prepared by mixing 1.44mM (GU)11G RNA and 1.44 mM NMM in 10 mM Tris, pH 7.03, and 100 mM KCl. An equal volume of RNA sample solution and reservoir solution were mixed and suspended over the reservoir solution consisting of 0.5 M Na/K tartarate, 0.1 M TrisHCl, pH 8.5, 5 mM NaOH. Cryoprotection: reservoir solution supplemented with 30% ethylene glycol. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.61 | 52.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.475 | α = 90 |
b = 42.483 | β = 90.09 |
c = 21.607 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | PIXEL | DECTRIS EIGER X 9M | 2020-09-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 1.1271 | APS | 21-ID-D |
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) | CC (Half) | 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 | 1.97 | 21.61 | 99.02 | 0.05163 | 0.05684 | 0.0231 | 0.998 | 16.09 | 6.7 | 5407 | 63.54 |
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 | 1.97 | 2.04 | 99.25 | 0.7553 | 0.8172 | 0.3083 | 0.966 | 1.57 | 6.9 |
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 | SAD | THROUGHOUT | 1.97 | 21.61 | 4922 | 476 | 97.35 | 0.27053 | 0.26869 | 0.29145 | RANDOM | 63.361 |
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] | |
20.86 | 9.54 | 9.07 | -29.93 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 10.721 |
r_long_range_B_refined | 6.788 |
r_long_range_B_other | 6.784 |
r_scangle_other | 4.182 |
r_scbond_it | 2.952 |
r_scbond_other | 2.949 |
r_angle_other_deg | 1.096 |
r_angle_refined_deg | 1.072 |
r_chiral_restr | 0.056 |
r_gen_planes_refined | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 493 |
Solvent Atoms | |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
AutoSol | phasing |