5Y9T

Crystal Structure of EGFR T790M mutant in complex with naquotinib


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IKA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M Hepes-Na 7.0-7.5, 1.3-1.5M potassium sodium tartrate
Crystal Properties
Matthews coefficientSolvent content
3.3363.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.64α = 90
b = 144.64β = 90
c = 144.64γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702011-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.25102.2899.90.10743.6110.28074-3
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)
13.253.321000.4149.7510.7

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 REPLACEMENTTHROUGHOUT3IKA3.25102.28769537299.730.197280.19520.24021RANDOM65.715
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.061
r_dihedral_angle_3_deg23.592
r_dihedral_angle_4_deg22.484
r_long_range_B_refined15.502
r_long_range_B_other15.501
r_mcangle_it8.819
r_mcangle_other8.816
r_scangle_other8.619
r_scbond_it5.587
r_mcbond_it5.548
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.061
r_dihedral_angle_3_deg23.592
r_dihedral_angle_4_deg22.484
r_long_range_B_refined15.502
r_long_range_B_other15.501
r_mcangle_it8.819
r_mcangle_other8.816
r_scangle_other8.619
r_scbond_it5.587
r_mcbond_it5.548
r_mcbond_other5.53
r_scbond_other5.527
r_dihedral_angle_1_deg5.157
r_angle_refined_deg1.711
r_angle_other_deg1.132
r_chiral_restr0.084
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.007
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2380
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing