Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with mRNA, A-site GGD-mutant Release Factor 1, and P-site fMEAAAKC-peptidyl-tRNAcys at 2.55A resolution
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8CVL | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION | 7.6 | 292 | 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.88 | 61.92 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 208.96 | α = 90 |
| b = 448.05 | β = 90 |
| c = 615.63 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 | DECTRIS EIGER2 X 16M | S/N E-32-0124 | 2023-03-11 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97911 | APS | 24-ID-C |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 2.55 | 122.56 | 98.6 | 0.149 | 0.17 | 0.993 | 8.01 | 4.247 | 1824998 | 55.627 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.55 | 2.62 | 99.5 | 1.596 | 1.832 | 0.204 | 0.9 | 4.033 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 8CVL | 2.55 | 122.56 | 1.35 | 1824739 | 91627 | 98.64 | 0.2178 | 0.2157 | 0.2177 | 0.2571 | 0.258 | 58.1486 | ||||
| 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 | 16.762 |
| f_angle_d | 0.847 |
| f_chiral_restr | 0.041 |
| f_plane_restr | 0.005 |
| f_bond_d | 0.004 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 94763 |
| Nucleic Acid Atoms | 195607 |
| Solvent Atoms | 4182 |
| Heterogen Atoms | 2707 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| Coot | model building |
| PDB_EXTRACT | data extraction |














