6YUL

CK2 alpha bound to Macrocycle


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PE2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.2 M ammonia sulphate, 0.1 MES pH 6.5, 31-35% (v/v) polyethylene glycol PEG 5000 MME 10 mg / mL protein
Crystal Properties
Matthews coefficientSolvent content
2.8757.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.649α = 90
b = 128.649β = 90
c = 125.454γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2018-09-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.999998SLSX06DA

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
12.445.481000.0270.99916.914.941786
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)
12.42.490.4260.718

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-VALUE3PE22.445.4841726206599.9760.2180.21680.232456.533
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]
0.210.21-0.421
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.73
r_dihedral_angle_4_deg16.248
r_dihedral_angle_3_deg14.888
r_lrange_it8.078
r_lrange_other8.078
r_dihedral_angle_1_deg6.428
r_scangle_it5.282
r_scangle_other5.26
r_mcangle_it4.993
r_mcangle_other4.993
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.73
r_dihedral_angle_4_deg16.248
r_dihedral_angle_3_deg14.888
r_lrange_it8.078
r_lrange_other8.078
r_dihedral_angle_1_deg6.428
r_scangle_it5.282
r_scangle_other5.26
r_mcangle_it4.993
r_mcangle_other4.993
r_scbond_it3.297
r_scbond_other3.275
r_mcbond_it3.108
r_mcbond_other3.107
r_angle_other_deg1.512
r_angle_refined_deg1.459
r_nbd_refined0.219
r_nbtor_refined0.178
r_symmetry_nbd_other0.174
r_symmetry_nbd_refined0.165
r_nbd_other0.165
r_symmetry_xyhbond_nbd_refined0.158
r_xyhbond_nbd_refined0.117
r_chiral_restr0.094
r_symmetry_nbtor_other0.08
r_ext_dist_refined_d0.048
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_symmetry_xyhbond_nbd_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5450
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing