3UG1
Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in the apo form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GS2 | PDB ENTRY 2GS2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | COUNTER-DIFFUSION | 7.1 | 293 | COUNTER DIFFUSION IN MICROGRAVITY CONDITIONS; COUNTER-DIFFUSION METHOD USING JAXA CRYSTALLISATION BOX (JCB). 40mm X 0.5mm CAPILLARIES WERE FILLED WITH 8.1mg/ml PROTEIN SOLUTION AND INSTALLED INTO JCB SYRINGE CASE FILLED WITH MOTHER LIQUOUR (1.7M Sodium CITRATE, 0.1M MES, 7.1). CRYSTALS WERE IN ORBIT FOR 2.5 MONTHS IN THE PROTEIN CRYSTALLISATION RESEARCH FACILITY ON THE JAPANESE EXPERIMENT MODULE OF THE INTERNATIONAL SPACE STATION., Counter Diffusion, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.09 | 60.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 141.334 | α = 90 |
b = 141.334 | β = 90 |
c = 141.334 | 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 | RAYONIX MX225HE | RHODIUM-COATED MIRRORS (HORIZONTAL AND VERTICAL) | 2009-10-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL41XU | 1.0 | SPring-8 | BL41XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.75 | 50 | 99.9 | 0.09 | 6.5 | 5.1 | 12348 | -3 | 67.04 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.75 | 2.9 | 100 | 0.42 | 1.8 | 5.1 | 1782 |
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 2GS2 | 2.75 | 50 | 12334 | 617 | 99.8 | 0.198 | 0.196 | 0.243 | RANDOM | 52.17 |
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 |
r_dihedral_angle_2_deg | 40.781 |
r_dihedral_angle_4_deg | 23.454 |
r_dihedral_angle_3_deg | 22.462 |
r_dihedral_angle_1_deg | 6.72 |
r_scangle_it | 4.294 |
r_scbond_it | 2.855 |
r_mcangle_it | 1.824 |
r_angle_refined_deg | 1.821 |
r_mcbond_it | 1.244 |
r_symmetry_hbond_refined | 0.346 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2301 |
Nucleic Acid Atoms | |
Solvent Atoms | 9 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |