3GTL
Backtracked RNA polymerase II complex with 13mer with G<>U mismatch
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.71 | 66.83 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 170.531 | α = 90 |
| b = 222.282 | β = 102.19 |
| c = 194.813 | 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 | MARMOSAIC 325 mm CCD | 2007-06-28 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.98 | SSRL | BL11-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.38 | 50 | 92.3 | 10.5 | 2.5 | 90557 | |||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 3.38 | 3.5 | 89.2 | 1.5 | 2.2 | ||||||||||||||
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 | PDB entry 3GTG | 3.38 | 50 | 85851 | 4515 | 91.06 | 0.27285 | 0.27028 | 0.32168 | RANDOM | 96.182 | ||||||
| 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] | |
| 1.57 | -11.68 | -4.39 | -2.11 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 39.538 |
| r_dihedral_angle_3_deg | 24.019 |
| r_dihedral_angle_4_deg | 18.674 |
| r_dihedral_angle_1_deg | 7.947 |
| r_scangle_it | 1.882 |
| r_angle_refined_deg | 1.613 |
| r_mcangle_it | 1.168 |
| r_scbond_it | 1.071 |
| r_mcbond_it | 0.656 |
| r_nbtor_refined | 0.319 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 28140 |
| Nucleic Acid Atoms | 1107 |
| Solvent Atoms | |
| Heterogen Atoms | 9 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MAR345 | data collection |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
