6CQH | pdb_00006cqh

Crystal Structure of the Human vaccinia-related kinase bound to a N-propynyl-N-ethyl-dihydropteridine inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629325% PEG3350, 300 mM LiSO4, 0.1M SBG, pH 6.0, 30% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.6253.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.492α = 90
b = 96.56β = 90
c = 193.395γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152017-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.968620APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.1529.6799.90.1810.2230.1280.996.55.394709
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.1999.91.021.2620.7320.6341.45.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OP52.1529.6789796483499.820.20260.200650.210.238850.24RANDOM30.416
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]
0.12-0.170.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.746
r_dihedral_angle_4_deg16.866
r_dihedral_angle_3_deg13.188
r_dihedral_angle_1_deg6.087
r_long_range_B_refined4.148
r_long_range_B_other4.148
r_angle_refined_deg1.307
r_angle_other_deg0.948
r_mcangle_it0.858
r_mcangle_other0.858
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.746
r_dihedral_angle_4_deg16.866
r_dihedral_angle_3_deg13.188
r_dihedral_angle_1_deg6.087
r_long_range_B_refined4.148
r_long_range_B_other4.148
r_angle_refined_deg1.307
r_angle_other_deg0.948
r_mcangle_it0.858
r_mcangle_other0.858
r_mcbond_it0.457
r_mcbond_other0.455
r_scangle_other0.452
r_scbond_it0.272
r_scbond_other0.272
r_chiral_restr0.077
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms9842
Nucleic Acid Atoms
Solvent Atoms644
Heterogen Atoms149

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing