6CMM | pdb_00006cmm

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529330.25% PEG3350, 200 mM LiSO4, 0.1M SBG buffer pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.5852.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.058α = 90
b = 95.753β = 90
c = 192.833γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.968610DiamondI24

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
12.129.7999.90.120.1420.0750.99810.96.7100045
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)
12.12.141001.1181.3440.7110.6911.56.6

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 REPLACEMENTTHROUGHOUT3OP52.129.7994907505299.90.191910.190290.20.222010.23RANDOM39.019
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]
0.710.32-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.822
r_dihedral_angle_4_deg16.941
r_dihedral_angle_3_deg13.634
r_dihedral_angle_1_deg6.169
r_long_range_B_refined4.497
r_long_range_B_other4.497
r_angle_refined_deg1.454
r_scangle_other1.063
r_angle_other_deg0.967
r_mcangle_it0.954
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.822
r_dihedral_angle_4_deg16.941
r_dihedral_angle_3_deg13.634
r_dihedral_angle_1_deg6.169
r_long_range_B_refined4.497
r_long_range_B_other4.497
r_angle_refined_deg1.454
r_scangle_other1.063
r_angle_other_deg0.967
r_mcangle_it0.954
r_mcangle_other0.954
r_scbond_it0.715
r_scbond_other0.715
r_mcbond_it0.562
r_mcbond_other0.547
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.007
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 Atoms9901
Nucleic Acid Atoms
Solvent Atoms474
Heterogen Atoms125

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing