6XI1
Crystal structure of tetra-tandem repeat in extending RTX adhesin from Aeromonas hydrophila
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | MICROBATCH | 4.6 | 294 | PEG 20,000, sodium acetate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.15 | 61.02 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 47.67 | α = 97.555 |
| b = 50.37 | β = 98.244 |
| c = 124.6 | γ = 101.719 |
| 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 | CCD | RAYONIX MX300HE | ultra-low expansion titanium siliicate flat mirror | 2016-02-12 | M | SINGLE WAVELENGTH | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.97949 | CLSI | 08ID-1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 1.75 | 48.64 | 97.3 | 0.081 | 0.094 | 0.048 | 0.998 | 10 | 3.9 | 108730 | 21.075 | ||||||||
| 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 | 1.75 | 1.78 | 95.3 | 0.83 | 0.96 | 0.483 | 0.859 | 1.9 | 4 | ||||||||||
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-Work | R-Free | Mean Isotropic B | ||||||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.75 | 48.638 | 108706 | 5436 | 97.26 | 0.183 | 0.1812 | 0.2098 | 25.274 | ||||||||
| 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] | |
| 0.474 | -1.677 | -1.366 | -1.162 | -2.253 | 2.643 | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.508 |
| r_dihedral_angle_3_deg | 10.45 |
| r_dihedral_angle_1_deg | 7.402 |
| r_lrange_it | 6.058 |
| r_lrange_other | 5.594 |
| r_scangle_it | 4.383 |
| r_scangle_other | 4.382 |
| r_scbond_it | 2.991 |
| r_scbond_other | 2.991 |
| r_mcangle_it | 2.876 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6012 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 974 |
| Heterogen Atoms | 114 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| AutoSol | phasing |
| PHENIX | model building |
| BUCCANEER | model building |
| Coot | model building |
