2YFX
Structure of L1196M Mutant Anaplastic Lymphoma Kinase in Complex with Crizotinib
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2XP2 | PDB ENTRY 2XP2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 286 | HANGING DROP VAPOR DIFFUSION AT 13 DEGREES C. EQUAL VOLUMES OF PURIFIED PROTEIN SOLUTION (APPROXIMATELY 7 MG/ML)CONTAINING 0.8 MM CRIZOTINIB WERE COMBINED WITH A SOLUTION CONTAINING: 0.15 M AMMONIUM SULFATE, 10% MONOMETHYLETHER PEG5K AND 0.1M MES PH 5.6. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.721 | α = 90 |
b = 57.174 | β = 90 |
c = 105.253 | 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 | 98 | PIXEL | DECTRIS PILATUS 6M | 2010-04-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.57 | 105.25 | 98.2 | 0.05 | 18.3 | 6.2 | 43152 | 1 | 23.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.57 | 1.66 | 91.5 | 0.34 | 2 | 2.2 |
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 | PDB ENTRY 2XP2 | 1.7 | 36.04 | 34791 | 1744 | 99.1 | 0.208 | 0.208 | 0.234 | RANDOM | 28.2 |
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] | |
-0.8 | -3.78 | 4.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 18.8 |
c_scangle_it | 3.58 |
c_scbond_it | 2.38 |
c_mcangle_it | 2.21 |
c_mcbond_it | 1.38 |
c_angle_deg | 0.8 |
c_improper_angle_d | 0.67 |
c_bond_d | 0.004 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2300 |
Nucleic Acid Atoms | |
Solvent Atoms | 237 |
Heterogen Atoms | 30 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
XDS | data reduction |
SCALA | data scaling |
CNX | phasing |