6NPN

Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OP5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629327.5% PEG 3350, 20 mM Li2SO4, 0.1M SBG, pH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.5952.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.53α = 90
b = 96.321β = 90
c = 191.108γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.968580DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.22099.80.2320.0680.99610.113.487245
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2299.91.9440.5750.6371.513.3

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 REPLACEMENTTHROUGHOUT3OP52.22082898427199.780.188350.186860.21796RANDOM34.773
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]
-0.341.5-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.883
r_dihedral_angle_4_deg19.154
r_dihedral_angle_3_deg13.62
r_long_range_B_refined6.843
r_long_range_B_other6.843
r_dihedral_angle_1_deg6.305
r_scangle_other5.338
r_mcangle_other4.342
r_mcangle_it4.34
r_scbond_it3.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.883
r_dihedral_angle_4_deg19.154
r_dihedral_angle_3_deg13.62
r_long_range_B_refined6.843
r_long_range_B_other6.843
r_dihedral_angle_1_deg6.305
r_scangle_other5.338
r_mcangle_other4.342
r_mcangle_it4.34
r_scbond_it3.575
r_scbond_other3.573
r_mcbond_it2.928
r_mcbond_other2.925
r_angle_refined_deg1.314
r_angle_other_deg0.945
r_chiral_restr0.068
r_bond_refined_d0.01
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 Atoms9723
Nucleic Acid Atoms
Solvent Atoms619
Heterogen Atoms223

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing