5IW7
Crystal structure of yeast Tsr1, a pre-40S ribosome synthesis factor
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6 | 291 | 8-14% w/v PEG 3350 0.18-0.30 M sodium malonate pH 6.0 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.38 | 63.64 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 65.687 | α = 90 |
| b = 174.199 | β = 90 |
| c = 320.474 | 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 PILATUS 6M | 2014-02-01 | M | SINGLE WAVELENGTH | ||||||
| 2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2014-11-26 | M | MAD | ||||||
| 3 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 6M | 2015-02-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.97 | Diamond | I03 |
| 2 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 1.255, 1.255, 1.254 | Diamond | I02 |
| 3 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 1.77 | Diamond | I04 |
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 | 3.6 | 48.77 | 99.9 | 0.127 | 14.4 | 10 | 43821 | 90.61 | |||||||||||
| 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 | 3.6 | 3.8 | 99.5 | 0.922 | 2.9 | 9.9 | |||||||||||||
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 3.6 | 48.77 | 43751 | 2228 | 99.93 | 0.2689 | 0.2675 | 0.295 | RANDOM | 87.09 | |||||||
| 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] | |
| -29.0988 | 4.3682 | 24.7306 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| t_other_torsion | 22.59 |
| t_omega_torsion | 1.96 |
| t_angle_deg | 0.99 |
| t_bond_d | 0.007 |
| t_dihedral_angle_d | |
| t_incorr_chiral_ct | |
| t_pseud_angle | |
| t_trig_c_planes | |
| t_gen_planes | |
| t_it | |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 16065 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| BUSTER | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| autoSHARP | phasing |
| PHENIX | phasing |
| PHASER | phasing |
