2ITU

Crystal structure of EGFR kinase domain L858R mutation in complex with AFN941


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M14PDB ENTRY 1M14

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.540% PEG400, 0.15M NACL, 0.1M HEPES 8.0, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
3.464

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.962α = 90
b = 144.962β = 90
c = 144.962γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM-42005-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

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
12.85099.90.0732.56.912764-3
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)
12.83.0299.70.393.56.1

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1M142.824.161197761699.80.2010.1980.258RANDOM63
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_deg42.094
r_dihedral_angle_4_deg21.792
r_dihedral_angle_3_deg20.051
r_dihedral_angle_1_deg7.012
r_scangle_it3.971
r_scbond_it2.34
r_mcangle_it2.12
r_angle_refined_deg1.889
r_mcbond_it1.122
r_nbtor_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.094
r_dihedral_angle_4_deg21.792
r_dihedral_angle_3_deg20.051
r_dihedral_angle_1_deg7.012
r_scangle_it3.971
r_scbond_it2.34
r_mcangle_it2.12
r_angle_refined_deg1.889
r_mcbond_it1.122
r_nbtor_refined0.333
r_nbd_refined0.263
r_symmetry_vdw_refined0.223
r_xyhbond_nbd_refined0.18
r_symmetry_hbond_refined0.144
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2417
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms35

Software

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