6G11
Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with the HMA domain of Pikp-1 from rice (Oryza sativa)
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.06M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate); 0.1M Buffer system 1 (1M Imidazole; MES monohydrate (acid)) pH 6.5; 50% v/v Precipitant mix 4 (25%v/v MPD; 25%v/v PEG 1000; 25%v/v PEG3350) |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.58 | 52.36 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 67.196 | α = 90 |
| b = 80.177 | β = 90 |
| c = 105.627 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
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 6M | 2016-12-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
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 | 1.9 | 46.29 | 100 | 0.1 | 14.5 | 12 | 45720 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 1.9 | 1.94 | |||||||||||||||||
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 | 5A6W | 1.9 | 46.29 | 43475 | 2178 | 99.89 | 0.20954 | 0.20876 | 0.22443 | RANDOM | 36.046 | ||||||
| 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] | |
| -2.96 | 4.84 | -1.88 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.236 |
| r_dihedral_angle_3_deg | 14.204 |
| r_dihedral_angle_4_deg | 9.889 |
| r_long_range_B_refined | 7.758 |
| r_long_range_B_other | 7.723 |
| r_dihedral_angle_1_deg | 6.235 |
| r_scangle_other | 5.667 |
| r_mcangle_it | 4.225 |
| r_mcangle_other | 4.225 |
| r_scbond_it | 3.713 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3436 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 227 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| xia2 | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
