2IVS

Crystal structure of non-phosphorylated RET tyrosine kinase domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GJOPDB ENTRY 1GJO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295PROTEIN 3 MG/ML IN 20 MM TRIS-HCL PH 8.0, 10MM NACL, 1MM DTT RESERVOIR 2.0 M SODIUM FORMATE, 0.1M SODIUM CITRATE PH 5.5 VAPOUR DIFFUSION, SITTING DROP,295 K
Crystal Properties
Matthews coefficientSolvent content
2.2247.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.399α = 90
b = 80.217β = 100.09
c = 79.684γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-09-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
1227.997.50.0816441522
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)
122.0780.60.25102

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 1GJO25039256208797.70.1830.180.229RANDOM21.26
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]
1.660.21-0.32-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.637
r_dihedral_angle_4_deg18.987
r_dihedral_angle_3_deg13.161
r_dihedral_angle_1_deg5.321
r_scangle_it3.979
r_scbond_it2.609
r_mcangle_it1.661
r_angle_refined_deg1.52
r_mcbond_it1.015
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.637
r_dihedral_angle_4_deg18.987
r_dihedral_angle_3_deg13.161
r_dihedral_angle_1_deg5.321
r_scangle_it3.979
r_scbond_it2.609
r_mcangle_it1.661
r_angle_refined_deg1.52
r_mcbond_it1.015
r_nbtor_refined0.306
r_nbd_refined0.198
r_symmetry_hbond_refined0.195
r_xyhbond_nbd_refined0.177
r_symmetry_vdw_refined0.166
r_chiral_restr0.105
r_bond_refined_d0.015
r_gen_planes_refined0.006
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 Atoms4311
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing