4WKQ | pdb_00004wkq

1.85 angstrom structure of EGFR kinase domain with gefitinib


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ITY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72910.1 M MES, pH 7.0, 1 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
3.2962.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.714α = 90
b = 143.714β = 90
c = 143.714γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85101.6299.919.440.642074
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8999.9120.3

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 REPLACEMENTTHROUGHOUT2ITY1.8510040025199799.80.195720.194240.20.224570.23RANDOM43.059
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_deg37.132
r_dihedral_angle_4_deg20.989
r_dihedral_angle_3_deg14.545
r_long_range_B_other6.325
r_long_range_B_refined6.324
r_dihedral_angle_1_deg6.175
r_scangle_other4.465
r_mcangle_it3.353
r_mcangle_other3.352
r_scbond_it2.905
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.132
r_dihedral_angle_4_deg20.989
r_dihedral_angle_3_deg14.545
r_long_range_B_other6.325
r_long_range_B_refined6.324
r_dihedral_angle_1_deg6.175
r_scangle_other4.465
r_mcangle_it3.353
r_mcangle_other3.352
r_scbond_it2.905
r_scbond_other2.905
r_mcbond_it2.208
r_mcbond_other2.198
r_angle_refined_deg1.685
r_angle_other_deg1.04
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms2317
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement