5TDJ
RNA decamer duplex with four 2'-5'-linkages
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4MS9 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 10% MPD (2-methyl-2,4-pentanediol), 40 mM sodium cacodylate pH 7.0, 12 mM spermine tetrahydrochloride, 40mM LiCl, 20 mM MgCl2 and 80 mM SrCl2 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.01 | 38.86 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 27.538 | α = 90 |
| b = 94.455 | β = 111.19 |
| c = 21.283 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2015-08-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.000 | ALS | 8.2.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | 1.5 | 30 | 96.7 | 0.064 | 18.3 | 3.9 | 7870 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.5 | 1.55 | 88.7 | 0.554 | 0.649 | 1.8 | 3 | ||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4MS9 | 1.5 | 19.9 | 7093 | 777 | 96.68 | 0.15385 | 0.15207 | 0.17033 | RANDOM | 33.663 | ||||||
| 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] | |
| -0.55 | -0.39 | 0.76 | 0.08 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_sphericity_free | 27.524 |
| r_sphericity_bonded | 24.542 |
| r_scangle_other | 10.465 |
| r_long_range_B_other | 8.673 |
| r_long_range_B_refined | 8.577 |
| r_scbond_it | 8.362 |
| r_scbond_other | 8.359 |
| r_rigid_bond_restr | 4.327 |
| r_angle_refined_deg | 1.962 |
| r_angle_other_deg | 1.823 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 424 |
| Solvent Atoms | 44 |
| Heterogen Atoms | 1 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
