5CYI

CDK2/Cyclin A covalent complex with 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-purin-2-amine (NU6300)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H1S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION277Protein at 5 mg per ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES (pH 7.0)
Crystal Properties
Matthews coefficientSolvent content
2.957.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.286α = 90
b = 135.289β = 90
c = 148.673γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1274.3499.90.1810.178.97.5101717
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)
122.0399.14.3280.57.2

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 REPLACEMENTTHROUGHOUT1H1S274.34101635491499.850.22810.22670.2548RANDOM52.6654
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]
-1.321.58-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.001
r_dihedral_angle_3_deg17.062
r_dihedral_angle_4_deg15.032
r_dihedral_angle_1_deg6.514
r_mcangle_it6.122
r_scbond_it4.187
r_mcbond_it3.96
r_angle_refined_deg1.742
r_chiral_restr0.106
r_bond_refined_d0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.001
r_dihedral_angle_3_deg17.062
r_dihedral_angle_4_deg15.032
r_dihedral_angle_1_deg6.514
r_mcangle_it6.122
r_scbond_it4.187
r_mcbond_it3.96
r_angle_refined_deg1.742
r_chiral_restr0.106
r_bond_refined_d0.013
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8947
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing