6YUM

CK2 alpha bound to unclosed Macrocycle


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M MES pH 6.5 0.2 ammonia sulphate 30% PEG 5000 MME 10 mg/mL protein
Crystal Properties
Matthews coefficientSolvent content
2.7154.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.479α = 90
b = 125.479β = 90
c = 124.655γ = 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 X06DA1.000031SLSX06DA

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
12.7544.3699.90.0450.99810.59.626481
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)
12.752.999.90.3160.923

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-VALUE3PE22.7544.3626427140799.7890.2640.26260.283868.329
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]
-0.185-0.1850.371
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.055
r_dihedral_angle_3_deg16.246
r_dihedral_angle_4_deg13.493
r_lrange_it7.686
r_lrange_other7.686
r_dihedral_angle_1_deg6.725
r_mcangle_it3.783
r_mcangle_other3.783
r_scangle_it3.387
r_scangle_other3.386
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.055
r_dihedral_angle_3_deg16.246
r_dihedral_angle_4_deg13.493
r_lrange_it7.686
r_lrange_other7.686
r_dihedral_angle_1_deg6.725
r_mcangle_it3.783
r_mcangle_other3.783
r_scangle_it3.387
r_scangle_other3.386
r_mcbond_it2.234
r_mcbond_other2.232
r_scbond_it1.935
r_scbond_other1.934
r_angle_other_deg1.5
r_angle_refined_deg1.376
r_nbd_refined0.219
r_nbd_other0.211
r_symmetry_xyhbond_nbd_refined0.185
r_nbtor_refined0.18
r_symmetry_nbd_other0.175
r_xyhbond_nbd_refined0.121
r_symmetry_nbd_refined0.112
r_ncsr_local_group_10.096
r_chiral_restr0.082
r_symmetry_nbtor_other0.079
r_ext_dist_refined_d0.044
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 Atoms5323
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing