6CNX | pdb_00006cnx

Crystal Structure of the Human vaccinia-related kinase 1 (VRK1) bound to an N-propynyl-N-isopentyl-dihydropteridin inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.1530.25% PEG3350, 30mM LiSO4, 0.1M SBG (Sodium-tartrate, Bis-Tris, Glycylglycine)
Crystal Properties
Matthews coefficientSolvent content
2.8156.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.47α = 90
b = 96.821β = 90
c = 192.831γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

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
122099.80.1360.0730.99310.25.1117261
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)
122.031001.0010.5650.5851.65.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OP5220111512566599.790.188250.187070.20.211120.22RANDOM31.898
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]
-0.320.52-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.163
r_dihedral_angle_4_deg17.049
r_dihedral_angle_3_deg12.683
r_dihedral_angle_1_deg6.165
r_long_range_B_refined5.08
r_long_range_B_other5.08
r_angle_refined_deg1.549
r_scangle_other1.536
r_mcangle_it1.409
r_mcangle_other1.409
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.163
r_dihedral_angle_4_deg17.049
r_dihedral_angle_3_deg12.683
r_dihedral_angle_1_deg6.165
r_long_range_B_refined5.08
r_long_range_B_other5.08
r_angle_refined_deg1.549
r_scangle_other1.536
r_mcangle_it1.409
r_mcangle_other1.409
r_angle_other_deg0.987
r_scbond_it0.944
r_scbond_other0.943
r_mcbond_it0.853
r_mcbond_other0.814
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms9866
Nucleic Acid Atoms
Solvent Atoms816
Heterogen Atoms202

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing