4FVR

Crystal structure of the Jak2 pseudokinase domain mutant V617F (Mg-ATP-bound form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FVPPDB ENTRY 4FVP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5277100 mM Tris/HCl, PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2144.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.9α = 90
b = 57.326β = 111.86
c = 60.555γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

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
11.755099.30.0666.36.429027
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)
11.751.7893.60.4315.31376

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 4FVP243.519530100695.50.18310.18060.229RANDOM36.77
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]
2.05-3.53-2.51-2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.082
r_dihedral_angle_4_deg18.649
r_dihedral_angle_3_deg14.689
r_dihedral_angle_1_deg6.718
r_angle_refined_deg1.281
r_angle_other_deg0.837
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.082
r_dihedral_angle_4_deg18.649
r_dihedral_angle_3_deg14.689
r_dihedral_angle_1_deg6.718
r_angle_refined_deg1.281
r_angle_other_deg0.837
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2147
Nucleic Acid Atoms
Solvent Atoms111
Heterogen Atoms32

Software

Software
Software NamePurpose
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-3000data reduction
HKL-3000data scaling