6Z83

CK2 alpha bound to chemical probe SGC-CK2-1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.9358.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.96α = 90
b = 126.96β = 90
c = 124.6γ = 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)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
12.1744.891000.99916.326.554337
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.172.230.761

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-VALUE6yul2.17144.8954265276799.9560.2160.2140.244636.336
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]
1.6481.648-3.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.756
r_dihedral_angle_4_deg17.312
r_dihedral_angle_3_deg15.056
r_dihedral_angle_1_deg6.276
r_lrange_it5.088
r_lrange_other5.088
r_scangle_it2.69
r_scangle_other2.689
r_mcangle_it2.452
r_mcangle_other2.452
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.756
r_dihedral_angle_4_deg17.312
r_dihedral_angle_3_deg15.056
r_dihedral_angle_1_deg6.276
r_lrange_it5.088
r_lrange_other5.088
r_scangle_it2.69
r_scangle_other2.689
r_mcangle_it2.452
r_mcangle_other2.452
r_scbond_it1.593
r_scbond_other1.593
r_angle_other_deg1.495
r_mcbond_other1.476
r_mcbond_it1.475
r_angle_refined_deg1.42
r_nbd_refined0.215
r_nbd_other0.209
r_symmetry_xyhbond_nbd_refined0.2
r_nbtor_refined0.18
r_symmetry_nbd_other0.179
r_symmetry_nbd_refined0.143
r_xyhbond_nbd_refined0.12
r_chiral_restr0.089
r_symmetry_nbtor_other0.081
r_ext_dist_refined_d0.044
r_bond_refined_d0.01
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 Atoms5441
Nucleic Acid Atoms
Solvent Atoms275
Heterogen Atoms165

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing