6I82

Crystal structure of partially phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018412


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.1 M sodium citrate pH 4.5-5.5, 2.0 M sodium formate drop size 500 nl + 500 nl RET at 3 mg/ml in 20 mM Tris pH 8.0, 100 mM NaCl, 1 mM DTT
Crystal Properties
Matthews coefficientSolvent content
2.2344.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.675α = 90
b = 80.336β = 99.87
c = 79.74γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.0545.8996.40.0817.53.138208
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.11750.470.731.32.1

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 REPLACEMENTTHROUGHOUT2IVS2.0545.8936312187696.330.178710.176010.22928RANDOM33.246
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]
2.581.11-1.03-1.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.956
r_dihedral_angle_4_deg21.742
r_dihedral_angle_3_deg16.772
r_long_range_B_refined7.694
r_long_range_B_other7.686
r_dihedral_angle_1_deg6.431
r_scangle_other5.876
r_mcangle_it4.217
r_mcangle_other4.217
r_scbond_it3.854
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.956
r_dihedral_angle_4_deg21.742
r_dihedral_angle_3_deg16.772
r_long_range_B_refined7.694
r_long_range_B_other7.686
r_dihedral_angle_1_deg6.431
r_scangle_other5.876
r_mcangle_it4.217
r_mcangle_other4.217
r_scbond_it3.854
r_scbond_other3.808
r_mcbond_other2.882
r_mcbond_it2.881
r_angle_refined_deg1.645
r_angle_other_deg1.28
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms4569
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms116

Software

Software
Software NamePurpose
GDAdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement