8QMI
Crystal structure of RNA G2C4 repeats - native model
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 8QMH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 292 | 0.08 M NaCl, 0.02 M Magnesium chloride hexahydrate, 0.04 M Na cacodylate trihydrate pH 6.0, 35% v/v MPD, 0.012 M Spermine tetrahydrochloride |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.68 | 26.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.759 | α = 90 |
b = 46.637 | β = 90 |
c = 51.492 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | PIXEL | RIGAKU HyPix-6000HE | 2020-10-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU PhotonJet-R | 1.54056 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.5 | 21.251 | 99.9 | 0.116 | 0.044 | 0.124 | 0.044 | 0.99 | 10 | 7.3 | 8334 |
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 | 1.5 | 1.58 | 100 | 0.553 | 0.276 | 0.276 | 0.846 | 2.4 |
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 (All) | R-Work | R-Free | Mean Isotropic B | ||||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.5 | 21.251 | 8309 | 404 | 99.628 | 0.171 | 0.1682 | 0.2255 | 8.629 |
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] | |
0.108 | 0.45 | -0.557 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_it | 4.039 |
r_lrange_other | 3.772 |
r_dihedral_angle_other_2_deg | 2.073 |
r_angle_refined_deg | 1.866 |
r_scangle_it | 1.274 |
r_scangle_other | 1.273 |
r_angle_other_deg | 1.195 |
r_scbond_it | 0.835 |
r_scbond_other | 0.835 |
r_symmetry_xyhbond_nbd_other | 0.714 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 492 |
Solvent Atoms | 108 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
SCALA | data scaling |
PHASER | phasing |