6GU3

CDK1/CyclinB/Cks2 in complex with AZD5438


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4Y72 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor
Crystal Properties
Matthews coefficientSolvent content
2.4249.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.636α = 90
b = 68.176β = 90
c = 167.324γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.987DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.6583.898.20.1293.421743
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.7895.30.821.93.4

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4Y722.6583.820615112897.830.198190.194850.25824RANDOM45.621
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]
-1.420.191.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.251
r_dihedral_angle_3_deg17.996
r_dihedral_angle_4_deg17.318
r_long_range_B_refined7.067
r_long_range_B_other7.066
r_dihedral_angle_1_deg6.393
r_scangle_other4.717
r_mcangle_it4.567
r_mcangle_other4.567
r_angle_other_deg3.653
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.251
r_dihedral_angle_3_deg17.996
r_dihedral_angle_4_deg17.318
r_long_range_B_refined7.067
r_long_range_B_other7.066
r_dihedral_angle_1_deg6.393
r_scangle_other4.717
r_mcangle_it4.567
r_mcangle_other4.567
r_angle_other_deg3.653
r_scbond_it2.835
r_scbond_other2.834
r_mcbond_it2.752
r_mcbond_other2.749
r_angle_refined_deg1.544
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_gen_planes_other0.006
r_bond_other_d
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 Atoms5139
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing