3UG2 | pdb_00003ug2

Crystal structure of the mutated EGFR kinase domain (G719S/T790M) in complex with gefitinib


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GS2PDB ENTRY 2GS2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12931.1M Sodium citrate, 0.1M MES PH 7.1, 5mg/ml protein, incubated overnight at 4deg with final concentration of 0.5mM gefitinib and 1% DMSO , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2562.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.675α = 90
b = 143.675β = 90
c = 143.675γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.545.451000.0935.745.317240-351.72
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.641000.4490.451.745.72503

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2GS22.545.45172088681000.190.1860.180.2490.25RANDOM39.47
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_deg40.655
r_dihedral_angle_4_deg20.719
r_dihedral_angle_3_deg19.233
r_dihedral_angle_1_deg6.81
r_scangle_it5.926
r_scbond_it4.374
r_mcangle_it2.456
r_angle_refined_deg2.202
r_mcbond_it1.792
r_nbtor_refined0.334
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.655
r_dihedral_angle_4_deg20.719
r_dihedral_angle_3_deg19.233
r_dihedral_angle_1_deg6.81
r_scangle_it5.926
r_scbond_it4.374
r_mcangle_it2.456
r_angle_refined_deg2.202
r_mcbond_it1.792
r_nbtor_refined0.334
r_symmetry_hbond_refined0.261
r_nbd_refined0.238
r_symmetry_vdw_refined0.227
r_xyhbond_nbd_refined0.179
r_chiral_restr0.127
r_bond_refined_d0.025
r_gen_planes_refined0.009
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2338
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms43

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling