RNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN S8/RRNA COMPLEX FROM METHANOCOCCUS JANNASCHII
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | ammonium sulphate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.79 | 74.34 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 121.687 | α = 90 |
| b = 121.687 | β = 90 |
| c = 137.975 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 110 | IMAGE PLATE | MARRESEARCH | 2000-05-17 | M | MAD | ||||||
| 2 | 1 | x-ray | 110 | IMAGE PLATE | MARRESEARCH | 2000-06-20 | M | MAD | ||||||
| 3 | 1 | x-ray | 110 | CCD | MARRESEARCH | 2000-06-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.97624,0.97933,0.97948 | ESRF | BM30A |
| 2 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.97949,0.97921,0.97435 | ESRF | BM30A |
| 3 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | 0.91 | EMBL/DESY, HAMBURG | X11 |
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 | ||||||||
| 1,2,3 | 2.57 | 41.07 | 91.3 | 0.045 | 13 | 7.5 | 30271 | 30271 | 64.3 | ||||||||||
| 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) | |||||||||||
| 2.57 | 2.71 | 82.5 | 0.249 | 5.8 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | 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) | R-Free Selection Details | Mean Isotropic B | |||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 2.6 | 41.07 | 2 | 29396 | 29179 | 1415 | 89.9 | 0.218 | 0.218 | 0.2206 | 0.251 | 0.2538 | RANDOM | 44.9 | |||
| 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] | |
| 3.77 | 3.77 | -7.54 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| c_dihedral_angle_d | 19 |
| c_scangle_it | 2.36 |
| c_mcangle_it | 2.21 |
| c_scbond_it | 1.53 |
| c_mcbond_it | 1.26 |
| c_improper_angle_d | 1.21 |
| c_angle_deg | 1.2 |
| c_bond_d | 0.006 |
| c_bond_d_na | |
| c_bond_d_prot | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2028 |
| Nucleic Acid Atoms | 1580 |
| Solvent Atoms | 215 |
| Heterogen Atoms | 20 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CNS | refinement |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| CNS | phasing |
