6NE7

Structure of G810A mutant of RET protein tyrosine kinase domain.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52992.2-2.6M Na FORMATE, 0.1M CITRATE pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.9257.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.286α = 90
b = 69.858β = 102.26
c = 78.971γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL14-11.1SSRLBL14-1

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.9939.196.60.790.950.05113.663.325551-324.92
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.02950.80.9730.5420.4581.33

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 REPLACEMENTTHROUGHOUT2IVT1.9939.124270128196.550.205590.203410.24921RANDOM38.123
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]
-0.020.010.03-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.24
r_dihedral_angle_4_deg18.823
r_dihedral_angle_3_deg16.022
r_long_range_B_refined8.157
r_dihedral_angle_1_deg5.841
r_mcangle_it4.504
r_scbond_it4.128
r_mcbond_it3.296
r_angle_refined_deg1.503
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.24
r_dihedral_angle_4_deg18.823
r_dihedral_angle_3_deg16.022
r_long_range_B_refined8.157
r_dihedral_angle_1_deg5.841
r_mcangle_it4.504
r_scbond_it4.128
r_mcbond_it3.296
r_angle_refined_deg1.503
r_chiral_restr0.093
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms2385
Nucleic Acid Atoms
Solvent Atoms133
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing