6CMS
Closed structure of active SHP2 mutant E76K bound to SHP099 inhibitor
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 9 | 291 | 100 mM bicine pH 9, 100 mM NaCl, 19 % PEG MME 550 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 37.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 40.715 | α = 90 |
b = 54.141 | β = 90 |
c = 218.847 | 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 | 2016-05-01 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | 2016-06-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.9795 | ALS | 8.2.2 |
2 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | 1.1270 | SSRL | BL14-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.68 | 72.95 | 99.3 | 0.981 | 6.2 | 13.4 | 14269 | 42.9596256648 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.68 | 2.83 | 94.9 | 0.874 | 2.6 | 13.8 |
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 | 2.68 | 54.71 | 1.33 | 14212 | 1420 | 99.23 | 0.2107 | 0.2046 | 0.2651 | 56.2 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.1003335969 |
f_angle_d | 0.511424802676 |
f_chiral_restr | 0.082522582629 |
f_plane_restr | 0.00224959665637 |
f_bond_d | 0.00204849580637 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3989 |
Nucleic Acid Atoms | |
Solvent Atoms | 67 |
Heterogen Atoms | 23 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
PHENIX | refinement |