X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING 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
238.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.314α = 90
b = 72.573β = 90
c = 72.038γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.98DiamondI24

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
11.1153.3189.80.080.9911.46.199386
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)
11.111.1344.30.770.551.42.6

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 REPLACEMENTTHROUGHOUT1HCK1.1151.1894432495489.720.166240.164870.19246RANDOM16.638
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]
0.86-0.37-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.779
r_rigid_bond_restr17.525
r_dihedral_angle_3_deg14.333
r_dihedral_angle_4_deg14.291
r_dihedral_angle_1_deg6.111
r_long_range_B_refined3.869
r_long_range_B_other3.868
r_scangle_other3.456
r_mcangle_it2.759
r_mcangle_other2.758
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.779
r_rigid_bond_restr17.525
r_dihedral_angle_3_deg14.333
r_dihedral_angle_4_deg14.291
r_dihedral_angle_1_deg6.111
r_long_range_B_refined3.869
r_long_range_B_other3.868
r_scangle_other3.456
r_mcangle_it2.759
r_mcangle_other2.758
r_scbond_other2.727
r_scbond_it2.726
r_angle_other_deg2.309
r_mcbond_it2.106
r_mcbond_other2.093
r_angle_refined_deg1.895
r_chiral_restr0.114
r_bond_other_d0.034
r_gen_planes_other0.016
r_bond_refined_d0.014
r_gen_planes_refined0.012
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 Atoms2330
Nucleic Acid Atoms
Solvent Atoms290
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing