5L2I

The X-ray co-crystal structure of human CDK6 and Palbociclib.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP286.151:1 (protein to well buffer) with well buffer containing: 0.1 M MES pH 6.0, 70 - 80 mM NH4NO3, 10 - 15% polyethyleneglycol 3350.
Crystal Properties
Matthews coefficientSolvent content
2.2545.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.749α = 90
b = 101.749β = 90
c = 60.778γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98.15PIXELDECTRIS PILATUS3 6M2013-08-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.755010014.66.88324100.71

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3NUX2.7537818783399.960.23460.22620.3037RANDOM92.38
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]
-8.0007-8.000716.0015
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.01
t_omega_torsion2.59
t_angle_deg1.16
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.01
t_omega_torsion2.59
t_angle_deg1.16
t_bond_d0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2085
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms33

Software

Software
Software NamePurpose
BUSTERrefinement
autoXDSdata processing
BUSTERphasing
Aimlessdata scaling