2ITV
Crystal structure of EGFR kinase domain L858R mutation in complex with AMP-PNP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1M14 | PDB ENTRY 1M14 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 40% PEG400, 0.15M NACL, 0.1M HEPES 7.5, pH 7.50 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.4 | 64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 145.081 | α = 90 |
b = 145.081 | β = 90 |
c = 145.081 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 CCD | 2005-10-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-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 | 2.47 | 50 | 99.7 | 0.06 | 45.6 | 7.2 | 18736 | -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 | 2.47 | 2.66 | 100 | 0.39 | 5.4 | 7.2 |
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 1M14 | 2.47 | 24.88 | 17364 | 940 | 99.8 | 0.197 | 0.195 | 0.242 | RANDOM | 54.14 |
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 |
r_dihedral_angle_2_deg | 41.581 |
r_dihedral_angle_3_deg | 18.004 |
r_dihedral_angle_4_deg | 16.982 |
r_dihedral_angle_1_deg | 6.31 |
r_scangle_it | 4.184 |
r_scbond_it | 2.527 |
r_mcangle_it | 2.064 |
r_angle_refined_deg | 1.7 |
r_mcbond_it | 1.109 |
r_nbtor_refined | 0.317 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2417 |
Nucleic Acid Atoms | |
Solvent Atoms | 149 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |