3GR0
Periplasmic domain of the T3SS inner membrane protein PrgH from S.typhimurium (fragment 170-362)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 30% (w/v) PEG 1500 + 0.1M lithium sulfate + 0.1M Tris 8.5 + 0.109M octanoyl-n-hydroxyethylglucamide, VAPOR DIFFUSION, HANGING DROP | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.52 | 51.18 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 53.257 | α = 90 |
| b = 53.257 | β = 90 |
| c = 282.527 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 31 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | CCD | ADSC QUANTUM 315 | M | SINGLE WAVELENGTH | ||||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | ALS | 8.2.2 | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 35 | 99.52 | 39588 | |||||||||||||||
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 | SAD | THROUGHOUT | 2.3 | 35 | 39588 | 2006 | 99.52 | 0.208 | 0.206 | 0.255 | RANDOM | 23.526 | |||||||
| 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] | |
| 1.24 | 0.62 | 1.24 | -1.86 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.269 |
| r_dihedral_angle_4_deg | 20.375 |
| r_dihedral_angle_3_deg | 17.45 |
| r_dihedral_angle_1_deg | 5.58 |
| r_scangle_it | 3.169 |
| r_scbond_it | 1.99 |
| r_angle_refined_deg | 1.328 |
| r_mcangle_it | 1.242 |
| r_mcbond_it | 0.761 |
| r_nbtor_refined | 0.303 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6080 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 231 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| SCALA | data scaling |
| SHARP | phasing |
