4FVQ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M14PDB ENTRY 1M14

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 = 44.632α = 90
b = 57.548β = 110.85
c = 60.967γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-11-03MSINGLE 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 1M141.7541.729014147199.190.1760.17480.1987RANDOM31.2572
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]
3.190.33-1.84-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.65
r_dihedral_angle_4_deg15.014
r_dihedral_angle_3_deg14.011
r_dihedral_angle_1_deg6.088
r_angle_refined_deg1.384
r_angle_other_deg0.862
r_chiral_restr0.08
r_bond_refined_d0.009
r_bond_other_d0.006
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.65
r_dihedral_angle_4_deg15.014
r_dihedral_angle_3_deg14.011
r_dihedral_angle_1_deg6.088
r_angle_refined_deg1.384
r_angle_other_deg0.862
r_chiral_restr0.08
r_bond_refined_d0.009
r_bond_other_d0.006
r_gen_planes_refined0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2135
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms40

Software

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