3D0X
Crystal Structure of the unbound lysine riboswitch
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | LITHIUM SULFATE, MAGNESIUM CHLORIDE, IRIDIUM HEXAMMINE, SODIUM HEPES | |||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.63 | 73.43 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 120.193 | α = 90 |
| b = 120.193 | β = 90 |
| c = 58.248 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 32 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2008-02-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
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 | 2.95 | 19.7 | 99.4 | 0.09 | 10.2 | 3.62 | 19610 | 55.12 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 2.95 | 3.06 | 100 | 0.355 | 3.4 | 3.63 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB entry 3D0U without lysine | 2.95 | 17.112 | 19610 | 1999 | 99.42 | 0.1907 | 0.1872 | 0.2203 | 54.92 | ||||||||
| 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] | |
| -7.97 | -7.97 | 15.941 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 19.332 |
| f_angle_d | 1.05 |
| f_chiral_restr | 0.069 |
| f_bond_d | 0.004 |
| f_plane_restr | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 3479 |
| Solvent Atoms | 60 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| d*TREK | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| CrystalClear | data collection |
| d*TREK | data reduction |
