6BP0

Crystal Structure of the Human vaccinia-related kinase 1 bound to (R)-2-phenylaminopteridinone inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729322% PEG3350; 0.02M Lithium Sulfate; 0.1M Buffer system SBG pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.5852.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.222α = 90
b = 95.118β = 90
c = 193.553γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152017-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979180APS24-ID-E

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
11.919.8199.20.1260.0510.9991313.7133129
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)
11.91.9398.61.9820.8130.5613

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 REPLACEMENTTHROUGHOUT3OP51.919.81126641643198.970.18860.18670.22589RANDOM37.609
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]
-0.052.39-2.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.305
r_dihedral_angle_4_deg16.066
r_dihedral_angle_3_deg12.251
r_long_range_B_refined6.124
r_long_range_B_other6.123
r_dihedral_angle_1_deg5.899
r_scangle_other3.758
r_mcangle_it3.063
r_mcangle_other3.063
r_scbond_it2.414
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.305
r_dihedral_angle_4_deg16.066
r_dihedral_angle_3_deg12.251
r_long_range_B_refined6.124
r_long_range_B_other6.123
r_dihedral_angle_1_deg5.899
r_scangle_other3.758
r_mcangle_it3.063
r_mcangle_other3.063
r_scbond_it2.414
r_scbond_other2.414
r_mcbond_it2.052
r_mcbond_other2.051
r_angle_refined_deg1.305
r_angle_other_deg0.933
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms9812
Nucleic Acid Atoms
Solvent Atoms1007
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing