4JQ8

Crystal structure of EGFR kinase domain in complex with compound 4b


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72911.0M Ammonium citrate tribase, 0.1M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.5265.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.745α = 90
b = 146.745β = 90
c = 146.745γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102011-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL12B21.0SPring-8BL12B2

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
12.833097.60.06914.05161271712717
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)
12.832.9399.20.4842.142.71240

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1M172.8330127171176660897.530.185910.183480.23233RANDOM60.045
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_deg37.61
r_dihedral_angle_3_deg16.424
r_dihedral_angle_4_deg11.081
r_dihedral_angle_1_deg5.828
r_angle_refined_deg1.265
r_angle_other_deg1.061
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.61
r_dihedral_angle_3_deg16.424
r_dihedral_angle_4_deg11.081
r_dihedral_angle_1_deg5.828
r_angle_refined_deg1.265
r_angle_other_deg1.061
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2409
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms39

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling