6YX5
Structure of DrrA from Legionella pneumophilia in complex with human Rab8a
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 9 | 293 | 0.1M bicine, pH 9, 2.4M ammonium sulphate |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.8 | 45 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 142.309 | α = 90 |
| b = 142.309 | β = 90 |
| c = 76.616 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 3 2 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 PILATUS 2M | 2018-09-07 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-1 | 0.966 | ESRF | MASSIF-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 | 2.14 | 48.06 | 99.7 | 0.2 | 0.206 | 0.045 | 0.99 | 15.57 | 20 | 49091 | 43.52 | ||||||||
| 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 | 2.14 | 2.22 | 96.97 | 2.43 | 2.5 | 0.57 | 0.43 | 0.93 | 18.3 | ||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 3NKU, 4LHV | 2.14 | 48.06 | 46650 | 2441 | 99.63 | 0.2084 | 0.2068 | 0.2385 | RANDOM | 50.306 | ||||||
| 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] | |
| -0.07 | -0.03 | -0.07 | 0.22 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.087 |
| r_dihedral_angle_4_deg | 16.777 |
| r_dihedral_angle_3_deg | 14.769 |
| r_dihedral_angle_1_deg | 6.091 |
| r_angle_refined_deg | 1.256 |
| r_angle_other_deg | 1.148 |
| r_chiral_restr | 0.05 |
| r_bond_refined_d | 0.004 |
| r_gen_planes_refined | 0.004 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4115 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 113 |
| Heterogen Atoms | 116 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data scaling |
| PHASER | phasing |
