6CMR
Closed structure of active SHP2 mutant E76D bound to SHP099 inhibitor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 15% PEG 20,000 and 10 mM potassium hydrogen tartrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 41.27 | α = 90 |
b = 54.36 | β = 90 |
c = 221.53 | γ = 90 |
Symmetry | |
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Space Group | P 2 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 | CCD | ADSC QUANTUM 315r | 2017-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.99997 | ALS | 8.2.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.21 | 52.79 | 99.92 | 0.1645 | 0.07346 | 0.993 | 5.85 | 6.1 | 25969 | 44.34 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.21 | 2.289 | 100 | 0.7128 | 6.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4DGP | 2.21 | 52.79 | 1.33 | 25954 | 3722 | 99.84 | 0.2271 | 0.2242 | 0.2605 | 58.13 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 9.9163 |
f_angle_d | 0.4569 |
f_chiral_restr | 0.0405 |
f_plane_restr | 0.0019 |
f_bond_d | 0.0016 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3850 |
Nucleic Acid Atoms | |
Solvent Atoms | 79 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
iMOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
PHENIX | refinement |