5UGC | pdb_00005ugc

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294Salt: 0.2 M Ammonium sulfate Precipitant: 19.5 %w/v PEG 8000 Buffer: 0.1 M HEPES (pH 7.50) Precipitant: 10.0 %v/v iso-propanol
Crystal Properties
Matthews coefficientSolvent content
1.831.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.722α = 90
b = 69.62β = 90
c = 112.029γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98CCDRAYONIX MX-3002014-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-11CLSI08ID-1

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
11.5843.641000.07620.45.943794525.7
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)
11.581.641000.9651.976

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5843.6437878186399.40.2010.1990.20.2230.22RANDOM30.5
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]
1.530.16-1.69
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.2
c_scangle_it2.72
c_scbond_it1.93
c_mcangle_it1.92
c_mcbond_it1.23
c_angle_deg0.8
c_improper_angle_d0.62
c_bond_d0.004
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.2
c_scangle_it2.72
c_scbond_it1.93
c_mcangle_it1.92
c_mcbond_it1.23
c_angle_deg0.8
c_improper_angle_d0.62
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 Atoms2321
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms32

Software

Software
Software NamePurpose
CNXrefinement
SCALEPACKdata scaling
CNXphasing
autoPROCdata scaling