5UG9

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-(propan-2-yl)-9H-purin-2-yl}pyrrolidin-3-yl]propanamide


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 294.0
Details Salt: 0.2 M Ammonium sulfate Precipitant: 14.1 %w/v PEG 8000 Buffer: 0.1 M HEPES (pH 7.50) Precipitant: 10.0 %v/v iso-propanol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.96 α = 90
b = 69.89 β = 90
c = 113.02 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 98
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 S 6M -- 2013-08-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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
1.33 113.02 100.0 -- 0.041 -- 6.4 -- 64321 -- -- 15.8
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.33 1.4 100.0 0.522 -- 3.0 6.3 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.33 59.45 -- 0.0 -- 64240 3144 99.5 -- 0.195 0.194 0.205 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.33 1.41 -- 480 9821 0.241 0.257 0.012 97.1
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.8
Anisotropic B[1][1] 2.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.81
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 1.78
c_scangle_it 2.59
c_angle_deg 0.8
c_dihedral_angle_d 18.9
c_improper_angle_d 0.65
c_mcangle_it 1.77
c_bond_d 0.004
c_mcbond_it 1.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.15
Luzzati Sigma A (Observed) 0.1
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.16
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2331
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 302

Software

Software
Software Name Purpose
CNX refinement version: 2005
SCALA data scaling
CNX phasing