8A27

EGFR kinase domain in complex with 2-(6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-1-yl)-2-[6-[2-[4-[[4-(hydroxymethyl)-1-piperidyl]methyl]phenyl]ethynyl]-1-oxo-4-(trifluoromethyl)isoindolin-2-yl]-N-thiazol-2-yl-acetamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HG8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629320% PEG Smear Medium, 0.1M MES, 0.15 ammonium nitrate, 5% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
1.8432.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.28α = 90
b = 34.915β = 128.92
c = 84.334γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-09-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9999SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.0765.6192.5113.1586262
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.071.160.66

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5hg81.0765.6186262454176.450.12620.12440.1599RANDOM16.31
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]
0.340.03-0.04-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.713
r_dihedral_angle_4_deg18.3
r_dihedral_angle_3_deg12.78
r_dihedral_angle_1_deg6.27
r_rigid_bond_restr6.127
r_angle_refined_deg2.082
r_angle_other_deg1.552
r_chiral_restr0.126
r_bond_refined_d0.018
r_gen_planes_refined0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.713
r_dihedral_angle_4_deg18.3
r_dihedral_angle_3_deg12.78
r_dihedral_angle_1_deg6.27
r_rigid_bond_restr6.127
r_angle_refined_deg2.082
r_angle_other_deg1.552
r_chiral_restr0.126
r_bond_refined_d0.018
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2159
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing