X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429310MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.1542.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.258α = 90
b = 72.337β = 90
c = 71.882γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.916DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.1172.341000.080.996.36.8110033
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.111.131002.540.350.46.5

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 REPLACEMENTTHROUGHOUT1HCK1.1142.92104562547199.940.211720.209770.24882RANDOM20.881
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]
-1.540.60.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.755
r_dihedral_angle_4_deg17.409
r_dihedral_angle_3_deg14.471
r_rigid_bond_restr13.828
r_dihedral_angle_1_deg5.986
r_scangle_other3.719
r_long_range_B_refined3.707
r_long_range_B_other3.707
r_scbond_it3.147
r_scbond_other3.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.755
r_dihedral_angle_4_deg17.409
r_dihedral_angle_3_deg14.471
r_rigid_bond_restr13.828
r_dihedral_angle_1_deg5.986
r_scangle_other3.719
r_long_range_B_refined3.707
r_long_range_B_other3.707
r_scbond_it3.147
r_scbond_other3.147
r_mcangle_it2.852
r_mcangle_other2.851
r_mcbond_other2.44
r_mcbond_it2.439
r_angle_other_deg2.327
r_angle_refined_deg2.007
r_chiral_restr0.109
r_bond_other_d0.033
r_gen_planes_other0.023
r_bond_refined_d0.014
r_gen_planes_refined0.013
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2277
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing