1W9H
The Structure of a Piwi protein from Archaeoglobus fulgidus.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 4.6 | PROTEIN SOLUTION AT 10 MG/ML WAS MIXED WITH A SOLUTION CONTAINING 0.1 M SODIUM ACETATE PH 4.6, 0.1 M CADMIUM CHLORIDE, 30% PEG 400, 5 MM DTT. CRYSTALS COULD BE OBTAINED REPRODUCIBLY BY STREAK SEEDING IN TO THE CRYSTALLISATION SOLUTION AFTER A 3 HOUR EQUILIBRATION. CRYSTALS APPEARED AFTER 2-3 DAYS AND GREW AFTER 5 DAYS TO A FINAL SIZE OF 0.1 MM X 0.1 MM X 0.1 MM | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.6 | 52.6 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 69.09 | ¦Á = 90 |
| b = 137.863 | ¦Â = 90 |
| c = 51.663 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 | 100 | CCD | MARRESEARCH | 2004-07-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-3 | ESRF | ID14-3 | |
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 | 1.95 | 30 | 98.6 | 0.05 | 18.6 | 4 | 143262 | ||||||||||||
| 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 | 1.95 | 2.05 | 92.8 | 0.16 | 6.4 | 3.2 | |||||||||||||
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 | 1.95 | 69.01 | 34383 | 1814 | 98.5 | 0.194 | 0.192 | 0.237 | RANDOM | 17.41 | |||||||
| 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] | |
| -0.95 | 1.83 | -0.88 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 40.712 |
| r_dihedral_angle_3_deg | 14.933 |
| r_dihedral_angle_4_deg | 12.412 |
| r_dihedral_angle_1_deg | 6.303 |
| r_scangle_it | 4.047 |
| r_scbond_it | 2.852 |
| r_mcangle_it | 1.8 |
| r_angle_refined_deg | 1.635 |
| r_mcbond_it | 1.188 |
| r_nbtor_refined | 0.314 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3233 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 238 |
| Heterogen Atoms | 11 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MOSFLM | data reduction |
| SCALA | data scaling |
| SnB | phasing |
| SHARP | phasing |
| REFMAC | refinement |
