6AAJ

Crystal structure of JAK2 in complex with peficitinib


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29350mM sodium citrate(pH6.5), 100mM ammonium phosphate, 20% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.7455.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.148α = 90
b = 126.657β = 96.49
c = 132.908γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS VII2014-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

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
12.3745.799.60.04316.43.828679
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)
12.372.4699.80.4942.23.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.3719.2427293138699.580.210740.208190.26163RANDOM59.196
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]
-0.02-0.01-0.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.632
r_dihedral_angle_4_deg19.181
r_dihedral_angle_3_deg18.332
r_long_range_B_refined9.576
r_dihedral_angle_1_deg6.271
r_mcangle_it5.709
r_scbond_it4.141
r_mcbond_it3.563
r_angle_refined_deg1.364
r_chiral_restr0.091
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.632
r_dihedral_angle_4_deg19.181
r_dihedral_angle_3_deg18.332
r_long_range_B_refined9.576
r_dihedral_angle_1_deg6.271
r_mcangle_it5.709
r_scbond_it4.141
r_mcbond_it3.563
r_angle_refined_deg1.364
r_chiral_restr0.091
r_bond_refined_d0.007
r_gen_planes_refined0.006
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_bond_other_d
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_sphericity_bonded
r_mcbond_other
r_angle_other_deg
r_mcangle_other
r_gen_planes_other
r_scbond_other
r_scangle_it
r_scangle_other
r_nbd_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4575
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing