3BKB

Crystal structure of human Feline Sarcoma Viral Oncogene Homologue (v-FES)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HYYAn ensemble of three kinase domains from the PDB entries 2HYY, 2G2I, 2G2H
experimental modelPDB 2G2IAn ensemble of three kinase domains from the PDB entries 2HYY, 2G2I, 2G2H
experimental modelPDB 2G2HAn ensemble of three kinase domains from the PDB entries 2HYY, 2G2I, 2G2H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2M Na2SO4, 0.1M Bis-Tris-Propane, 20% PEG 3350, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.8757.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.404α = 90
b = 80.404β = 90
c = 131.411γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.98074SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.7843.811000.1280.12818.714.14601946019
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.781.881000.7870.78725.96704

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAn ensemble of three kinase domains from the PDB entries 2HYY, 2G2I, 2G2H1.7843.814597745977231299.930.150.150.1480.189RANDOM21.662
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]
0.390.190.39-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.042
r_dihedral_angle_4_deg12.284
r_dihedral_angle_3_deg12.098
r_dihedral_angle_1_deg5.941
r_mcbond_it3.545
r_angle_refined_deg1.532
r_angle_other_deg1.118
r_mcbond_other0.942
r_symmetry_vdw_other0.265
r_nbd_refined0.204
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.042
r_dihedral_angle_4_deg12.284
r_dihedral_angle_3_deg12.098
r_dihedral_angle_1_deg5.941
r_mcbond_it3.545
r_angle_refined_deg1.532
r_angle_other_deg1.118
r_mcbond_other0.942
r_symmetry_vdw_other0.265
r_nbd_refined0.204
r_nbd_other0.202
r_symmetry_hbond_refined0.178
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.158
r_chiral_restr0.105
r_nbtor_other0.085
r_symmetry_vdw_refined0.078
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_mcangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2927
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms82

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction