2IVU

Crystal structure of phosphorylated RET tyrosine kinase domain complexed with the inhibitor ZD6474


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherIN-HOUSE PART-REFINED STRUCTURE OF RET KINASE DOMAIN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289PROTEIN 3 MG/ML IN 20 MM TRIS-HCL PH 8.0, 100MM NACL, 1MM DTT, 1MM EDTA, 1MM SODIUM VANADATE RESERVOIR 2.2 M SODIUM FORMATE, 0.1M SODIUM ACETATE PH 4.5 VAPOUR DIFFUSION, SITTING DROP, 289 K
Crystal Properties
Matthews coefficientSolvent content
2.7557.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.409α = 90
b = 71.42β = 101.23
c = 78.834γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2005-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.515.399.60.069.63.713506
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)
12.52.6499.60.164.63.7

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 REPLACEMENTTHROUGHOUTIN-HOUSE PART-REFINED STRUCTURE OF RET KINASE DOMAIN2.5501283567099.50.1930.190.248RANDOM35.62
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]
0.230.250.2-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.199
r_dihedral_angle_4_deg20.204
r_dihedral_angle_3_deg15.589
r_dihedral_angle_1_deg5.924
r_scangle_it3.368
r_scbond_it2.279
r_angle_refined_deg1.614
r_mcangle_it1.537
r_mcbond_it0.915
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.199
r_dihedral_angle_4_deg20.204
r_dihedral_angle_3_deg15.589
r_dihedral_angle_1_deg5.924
r_scangle_it3.368
r_scbond_it2.279
r_angle_refined_deg1.614
r_mcangle_it1.537
r_mcbond_it0.915
r_nbtor_refined0.306
r_symmetry_vdw_refined0.202
r_nbd_refined0.193
r_xyhbond_nbd_refined0.154
r_chiral_restr0.104
r_symmetry_hbond_refined0.072
r_bond_refined_d0.015
r_gen_planes_refined0.005
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 Atoms2189
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing