8G8O

The crystal structure of JAK2 in complex with Compound 31


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IOK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 3350, ammonium acetate, HEPES
Crystal Properties
Matthews coefficientSolvent content
2.1442.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.58α = 90
b = 179.56β = 110.53
c = 52.21γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.247.1899.90.1750.0758.26.531923
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.271.3190.5341.5

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 REPLACEMENTTHROUGHOUT3IOK2.247.1830285159799.820.189480.187270.23127RANDOM38.111
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]
-5.990.3313.81-7.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.062
r_dihedral_angle_4_deg21.861
r_dihedral_angle_3_deg17.403
r_long_range_B_other9.889
r_long_range_B_refined9.885
r_dihedral_angle_1_deg6.642
r_scangle_other6.032
r_mcangle_it5.656
r_mcangle_other5.656
r_scbond_it4.153
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.062
r_dihedral_angle_4_deg21.861
r_dihedral_angle_3_deg17.403
r_long_range_B_other9.889
r_long_range_B_refined9.885
r_dihedral_angle_1_deg6.642
r_scangle_other6.032
r_mcangle_it5.656
r_mcangle_other5.656
r_scbond_it4.153
r_scbond_other4.153
r_mcbond_it3.975
r_mcbond_other3.972
r_angle_refined_deg1.623
r_angle_other_deg1.24
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4625
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata scaling
PHASERphasing