6UXT
Crystal structure of unknown function protein yfdX from Shigella flexneri
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6A02 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 6 | 297 | 20% PEG3350, 0.2M ammonium citrate, 50mM MES |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.69 | 54.24 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 51.579 | α = 97.35 |
| b = 92.92 | β = 98.44 |
| c = 93.469 | γ = 95.46 |
| Symmetry | |
|---|---|
| Space Group | P 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 | PIXEL | DECTRIS PILATUS3 X 6M | 2019-06-11 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97918 | APS | 19-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.797 | 50 | 91.4 | 0.062 | 0.073 | 0.037 | 7.1 | 3.7 | 143645 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 1.8 | 1.83 | 91.4 | 0.477 | 0.562 | 0.296 | 0.823 | 3.5 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Free (Depositor) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6A02 | 1.797 | 43.517 | 1.98 | 143610 | 7201 | 91.1 | 0.1716 | 0.1701 | 0.2003 | 32.3239 | ||||||
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 10010 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 753 |
| Heterogen Atoms | 42 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| SCALEPACK | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | phasing |
