2X2M

Crystal Structure of phosphorylated RET tyrosine kinase domain with inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IVTPDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289PROTEIN 4.5 MG/ML IN 20 MM TRIS-HCL PH 8, 100MM NACL, 1MM DTT, 1MM EDTA RESERVOIR 1.75 M SODIUM FORMATE, 0.1 SODIUM CITRATE PH 5.5, 0.15 M POTASSIUM THIOCYANATE VAPOUR DIFFUSION, SITTING DROP, 289 K
Crystal Properties
Matthews coefficientSolvent content
2.7254.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.697α = 103.5
b = 50.76β = 99.66
c = 74.588γ = 89.92
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS2007-08-03MSINGLE 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
12.518.9995.40.0411.92.22352448
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)
12.52.6493.90.116.62.21

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED2.53022326119795.50.203270.201140.24162RANDOM28.346
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]
0.20.430.630.71.02-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.612
r_dihedral_angle_4_deg18.952
r_dihedral_angle_3_deg16.289
r_dihedral_angle_1_deg5.533
r_scangle_it2.928
r_scbond_it1.856
r_angle_refined_deg1.562
r_mcangle_it1.365
r_mcbond_it0.79
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.612
r_dihedral_angle_4_deg18.952
r_dihedral_angle_3_deg16.289
r_dihedral_angle_1_deg5.533
r_scangle_it2.928
r_scbond_it1.856
r_angle_refined_deg1.562
r_mcangle_it1.365
r_mcbond_it0.79
r_nbtor_refined0.309
r_symmetry_vdw_refined0.308
r_xyhbond_nbd_refined0.244
r_nbd_refined0.211
r_symmetry_hbond_refined0.201
r_chiral_restr0.098
r_bond_refined_d0.014
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 Atoms4327
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing