2OLT
Crystal structure of a phou-like protein (so_3770) from shewanella oneidensis mr-1 at 2.00 A resolution
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.8 | 277 | NANODROP, 1.5M Sodium acetate, 0.1M Sodium cacodylate pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
| 2 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 277 | NANODROP, 1.0M Sodium citrate, 0.1M Sodium cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 99.53 | α = 90 |
| b = 99.53 | β = 90 |
| c = 395.92 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 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 | ADSC QUANTUM 315 | 2006-09-14 | M | SINGLE WAVELENGTH | ||||||
| 2 | 2 | x-ray | 100 | CCD | ADSC QUANTUM 315 | Flat mirror (vertical focusing) | 2006-05-07 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 1.00000 | ALS | 8.2.2 |
| 2 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.918370, 0.979318, 0.979035 | SSRL | BL11-1 |
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 | 2 | 29.16 | 99.9 | 0.058 | 13.4 | 5.5 | 51605 | 36 | |||||||||||
| 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 | 2 | 2.05 | 100 | 0.623 | 5.5 | 3630 | |||||||||||||
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MAD | THROUGHOUT | 2 | 29.16 | 51591 | 2634 | 99.84 | 0.205 | 0.205 | 0.203 | 0.242 | RANDOM | 39.759 | ||||||
| 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] | |
| 2.45 | 1.22 | 2.45 | -3.67 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 31.873 |
| r_dihedral_angle_3_deg | 12.753 |
| r_dihedral_angle_4_deg | 10.545 |
| r_scangle_it | 3.815 |
| r_dihedral_angle_1_deg | 2.981 |
| r_scbond_it | 2.459 |
| r_angle_refined_deg | 1.565 |
| r_mcangle_it | 1.353 |
| r_angle_other_deg | 1.006 |
| r_mcbond_it | 0.956 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4898 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 381 |
| Heterogen Atoms | 27 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| MolProbity | model building |
| SHELX | phasing |
| REFMAC | refinement |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| DENZO | data reduction |
| SHARP | phasing |
