Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 3DVZ | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 291.15 | 0.233 mM RNA, 1.0 M ammonium sulfate, 2 mM magnesium chloride, 2 mM manganese chloride, 16.5 mM -3-(N-morpholino)propanesulfonic acid. |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 1.9 | 35.37 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 29.495 | α = 90 |
| b = 29.495 | β = 90 |
| c = 76.52 | γ = 90 |
Diffraction
| Diffraction Experiment |
|---|
| 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 | | 2020-02-14 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 100 | AREA DETECTOR | ORNL ANGER CAMERA | | 2020-01-29 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | LIQUID ANODE | Excillum MetalJet D2 70 kV | 1.342 | | |
| 2 | SPALLATION SOURCE | ORNL Spallation Neutron Source BEAMLINE MANDI | 2.0-4.0 | ORNL Spallation Neutron Source | MANDI |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 0.998 | 16.05 | 99.67 | 0.055 | | | | 0.999 | | 21.66 | 13.68 | | 35326 | | | 8.3 |
| 2 | 2.25 | 12.34 | 92.32 | 0.212 | | | | 0.886 | | 9.8 | 3.4 | | 2887 | | | 8.3 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 0.998 | 1.033 | | 0.412 | | | | 0.849 | | | | |
| 2 | 2.25 | 2.33 | | 0.299 | | | | 0.3 | | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1 | 16.05 | | 1.34 | | 35272 | 3483 | 99.42 | | 0.1812 | 0.1785 | 0.18 | 0.1965 | 0.2 | | 17.21 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.25 | 12.34 | | | | 2886 | | 92.32 | | | 0.2543 | | 0.2987 | | | |
| 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 |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 23.333 |
| f_angle_d | 1.6111 |
| f_chiral_restr | 0.1076 |
| f_plane_restr | 0.0129 |
| f_bond_d | 0.0115 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | |
| Nucleic Acid Atoms | 579 |
| Solvent Atoms | 80 |
| Heterogen Atoms | 5 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| PROTEUM PLUS | data reduction |
| PROTEUM PLUS | data scaling |
| PHENIX | phasing |
