6ZW3
Racemic compound of RNA duplexes.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyethylene glycol 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2 | 38.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 20.95 | α = 106.033 |
b = 26.49 | β = 96.057 |
c = 38.66 | γ = 92.598 |
Symmetry | |
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Space Group | P 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 PILATUS 6M | 2018-12-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 1.283 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim 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 | 1.52 | 37 | 86.7 | 0.168 | 0.198 | 0.975 | 4.19 | 3.5 | 10572 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.52 | 1.61 | 1.061 | 1.252 | 0.652 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 6ZQ9 | 1.522 | 36.874 | 10553 | 563 | 86.756 | 0.216 | 0.2128 | 0.2721 | 20.915 |
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] | |
-0.731 | 0.709 | 0.242 | 1.541 | 0.039 | -0.802 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_lrange_it | 6.742 |
r_lrange_other | 5.432 |
r_scangle_it | 1.873 |
r_scangle_other | 1.872 |
r_angle_refined_deg | 1.436 |
r_scbond_it | 1.304 |
r_scbond_other | 1.303 |
r_angle_other_deg | 1.182 |
r_symmetry_xyhbond_nbd_other | 0.318 |
r_symmetry_nbd_other | 0.272 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 676 |
Solvent Atoms | 187 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |