2ITT | pdb_00002itt

Crystal structure of EGFR kinase domain L858R mutation in complex with AEE788


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M17PDB ENTRY 1M17

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.540% PEG400, 0.15M NACL, 0.1M HEPES 8.0, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
3.464

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 145.717α = 90
b = 145.717β = 90
c = 145.717γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM-42005-08-05MSINGLE 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
12.735099.80.0536.26.113877-3
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)
12.732.9499.80.374.34.9

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1M172.7324.991278398799.60.2120.2080.210.2620.26RANDOM56.8
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_deg41.052
r_dihedral_angle_3_deg19.498
r_dihedral_angle_4_deg17.081
r_dihedral_angle_1_deg6.943
r_scangle_it3.994
r_scbond_it2.387
r_mcangle_it2.094
r_angle_refined_deg1.809
r_mcbond_it1.141
r_nbtor_refined0.327
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.052
r_dihedral_angle_3_deg19.498
r_dihedral_angle_4_deg17.081
r_dihedral_angle_1_deg6.943
r_scangle_it3.994
r_scbond_it2.387
r_mcangle_it2.094
r_angle_refined_deg1.809
r_mcbond_it1.141
r_nbtor_refined0.327
r_nbd_refined0.244
r_xyhbond_nbd_refined0.211
r_symmetry_hbond_refined0.196
r_symmetry_vdw_refined0.193
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.006
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 Atoms2413
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms33

Software

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