6R8M
Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with an engineered HMA domain of Pikp-1 from rice (Oryza sativa)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6G10 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | Morpheus HT-96 condition A8 [0.06M Divalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate); 0.1M Buffer system 2 (Sodium HEPES; MOPS (acid)) pH 7.5; 37.5%v/v Precipitant mix 4 (25%v/v MPD; 25%v/v PEG 1000; 25%v/v PEG3350) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.58 | 52.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.456 | α = 90 |
b = 80.701 | β = 90 |
c = 105.577 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9763 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.85 | 29.5 | 99.8 | 0.052 | 0.054 | 0.017 | 1 | 31 | 18.3 | 49337 |
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 | 1.85 | 1.89 | 97.8 | 0.751 | 0.773 | 0.181 | 0.952 | 17.8 |
Refinement
Statistics | |||||||||||||||||||
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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 | 6G10 | 1.85 | 29.5 | 46754 | 2518 | 99.81 | 0.1886 | 0.1864 | 0.2301 | RANDOM | 38.435 |
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] | |
-1.9 | 4.1 | -2.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.764 |
r_dihedral_angle_4_deg | 18.71 |
r_dihedral_angle_3_deg | 15.116 |
r_dihedral_angle_1_deg | 7.102 |
r_angle_refined_deg | 1.558 |
r_angle_other_deg | 1.316 |
r_chiral_restr | 0.07 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3546 |
Nucleic Acid Atoms | |
Solvent Atoms | 294 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |