Crystal structure of tWHD1 of Rpc5 subunit of human RNA Polymerase III
Serial Crystallography (SX)
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | | 277 | 3.2 M NaCl, 100 mM Sodium Acetate pH 4.6 and 10 mM ZnCl2 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 56.3 | α = 90 |
| b = 56.3 | β = 90 |
| c = 275.88 | γ = 120 |
| Symmetry |
|---|
| Space Group | P 61 2 2 |
|---|
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 PILATUS3 6M | | 2014-11-19 | M | SINGLE WAVELENGTH |
| 2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | | 2015-02-13 | M | MAD |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9198 | Diamond | I04 |
| 2 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97965, 0.97980, 0.971970 | Diamond | I03 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 2 | | fixed target |
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 | 2.23 | 48.01 | 100 | 0.05 | 26.9 | 27.4 | | 13725 | | | |
| 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) |
|---|
| 1 | 2.23 | 2.31 | | | 0.749 | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MAD | FREE R-VALUE | 2.23 | 45.97 | 13725 | | 100 | 0.18 | 0.19 | 0.22 | 0.23 | 50.97 |
| 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 | 16.0104 |
| f_angle_d | 0.8413 |
| f_chiral_restr | 0.053 |
| f_bond_d | 0.0078 |
| f_plane_restr | 0.0047 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1354 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 121 |
| Heterogen Atoms | 4 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| PHENIX | phasing |