3VRN

Crystal structure of the tyrosine kinase binding domain of Cbl-c


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729316% PEG3350, 0.1M ammonium formate, 0.2M NDSB-201, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8734.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.223α = 90
b = 107.617β = 90
c = 54.773γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDBruker DIP-60402007-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900SPring-8BL44XU

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
11.64501000.0540.05427.9924.334203-317.8
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)
11.641.671000.4460.4463.4524.31688

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 REPLACEMENTTHROUGHOUT2CBL1.6443.2434184172899.810.18340.18160.2177RANDOM20.2597
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.362
r_dihedral_angle_3_deg13.697
r_dihedral_angle_4_deg13.063
r_scangle_it5.727
r_dihedral_angle_1_deg5.316
r_scbond_it3.727
r_mcangle_it2.404
r_angle_refined_deg1.849
r_mcbond_it1.358
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.362
r_dihedral_angle_3_deg13.697
r_dihedral_angle_4_deg13.063
r_scangle_it5.727
r_dihedral_angle_1_deg5.316
r_scbond_it3.727
r_mcangle_it2.404
r_angle_refined_deg1.849
r_mcbond_it1.358
r_chiral_restr0.127
r_bond_refined_d0.022
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2270
Nucleic Acid Atoms
Solvent Atoms239
Heterogen Atoms1

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction