8A2D

EGFR kinase domain (L858R/V948R) in complex with 2-[4-(difluoromethyl)-6-[2-[4-[[4-(hydroxymethyl)-1-piperidyl]methyl]phenyl]ethynyl]-7-methyl-indazol-2-yl]-2-spiro[6,7-dihydropyrrolo[1,2-c]imidazole-5,1'-cyclopropane]-1-yl-N-thiazol-2-yl-acetamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8A27 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529320% PEG Smear High, 0.1M MES
Crystal Properties
Matthews coefficientSolvent content
1.831.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.619α = 90
b = 34.951β = 128.81
c = 83.934γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-09-12MSINGLE 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
11.1165.490.3111.23.690192
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)
11.121.160.67

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 REPLACEMENTTHROUGHOUT8A271.1165.490192472289.670.1640.16320.1788RANDOM15.73
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]
0.140.09-0.330.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.572
r_dihedral_angle_4_deg17.761
r_dihedral_angle_3_deg14.141
r_dihedral_angle_1_deg6.42
r_angle_refined_deg2.278
r_angle_other_deg1.54
r_chiral_restr0.133
r_bond_refined_d0.021
r_gen_planes_refined0.013
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.572
r_dihedral_angle_4_deg17.761
r_dihedral_angle_3_deg14.141
r_dihedral_angle_1_deg6.42
r_angle_refined_deg2.278
r_angle_other_deg1.54
r_chiral_restr0.133
r_bond_refined_d0.021
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2276
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing