5UG8

Crystal structure of the EGFR kinase domain (L858R, T790M, V948R) in complex with a covalent inhibitor N-[(3R,4R)-4-fluoro-1-{6-[(1-methyl-1H-pyrazol-4-yl)amino]-9-(propan-2-yl)-9H-purin-2-yl}pyrrolidin-3-yl]propanamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP286Salt: 0.2 M Ammonium sulfate Precipitant: 11.4 %w/v PEG 8000 Buffer: 0.1 M HEPES (pH 7.50) Precipitant: 10.0 %v/v iso-propanol
Crystal Properties
Matthews coefficientSolvent content
1.8433.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.948α = 90
b = 69.836β = 90
c = 113.252γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98PIXELDECTRIS PILATUS3 S 6M2013-06-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.4659.4499.90.05816.26.44918920
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.461.541000.4863.26.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.4659.4449060243299.90.1930.1920.207RANDOM23.1
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]
3.59-2.64-0.95
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.1
c_scangle_it2.8
c_scbond_it1.94
c_mcangle_it1.91
c_mcbond_it1.17
c_angle_deg0.8
c_improper_angle_d0.64
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.1
c_scangle_it2.8
c_scbond_it1.94
c_mcangle_it1.91
c_mcbond_it1.17
c_angle_deg0.8
c_improper_angle_d0.64
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2320
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms34

Software

Software
Software NamePurpose
CNXrefinement
SCALAdata scaling
CNXphasing