6Z84

CK2 alpha bound to chemical probe SGC-CK2-1 derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YUL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M bis-tris pH 5.5 23-26% (v/v) PEG 3350 0.2 M ammonia sulphate
Crystal Properties
Matthews coefficientSolvent content
3.0860.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.352α = 90
b = 126.352β = 90
c = 124.514γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2020-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.99999SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.544.671000.0560.99812.713.235531
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.60.4150.8452

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6yul2.544.6735475185099.9690.2170.2150.250139.771
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]
2.3622.362-4.723
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.021
r_dihedral_angle_4_deg18.479
r_dihedral_angle_3_deg15.502
r_dihedral_angle_1_deg6.248
r_lrange_it4.587
r_lrange_other4.525
r_mcangle_it2.667
r_mcangle_other2.667
r_scangle_other2.563
r_scangle_it2.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.021
r_dihedral_angle_4_deg18.479
r_dihedral_angle_3_deg15.502
r_dihedral_angle_1_deg6.248
r_lrange_it4.587
r_lrange_other4.525
r_mcangle_it2.667
r_mcangle_other2.667
r_scangle_other2.563
r_scangle_it2.56
r_mcbond_it1.556
r_mcbond_other1.556
r_angle_other_deg1.49
r_scbond_it1.482
r_scbond_other1.482
r_angle_refined_deg1.406
r_nbd_refined0.218
r_nbd_other0.211
r_symmetry_nbd_refined0.187
r_symmetry_nbd_other0.181
r_nbtor_refined0.18
r_symmetry_xyhbond_nbd_refined0.124
r_xyhbond_nbd_refined0.118
r_chiral_restr0.088
r_symmetry_nbtor_other0.08
r_ext_dist_refined_d0.051
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5415
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing