6Q4K

CDK2 in complex with FragLite38


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
1.9537.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.897α = 90
b = 71.265β = 90
c = 72.062γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.98DiamondI04

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
11.0672.0784.30.0260.9924.75.7105138
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)
11.061.085.50.560.610.81.1

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 REPLACEMENTTHROUGHOUT1HCK1.0650.7299908523084.270.144070.143120.16216RANDOM19.66
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]
-0.560.59-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.591
r_dihedral_angle_4_deg13.813
r_dihedral_angle_3_deg13.282
r_rigid_bond_restr11.882
r_dihedral_angle_1_deg6.185
r_long_range_B_refined4.673
r_long_range_B_other4.673
r_scangle_other4.041
r_scbond_it3.343
r_scbond_other3.342
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.591
r_dihedral_angle_4_deg13.813
r_dihedral_angle_3_deg13.282
r_rigid_bond_restr11.882
r_dihedral_angle_1_deg6.185
r_long_range_B_refined4.673
r_long_range_B_other4.673
r_scangle_other4.041
r_scbond_it3.343
r_scbond_other3.342
r_mcangle_it2.99
r_mcangle_other2.989
r_angle_other_deg2.321
r_mcbond_it2.317
r_mcbond_other2.312
r_angle_refined_deg1.881
r_chiral_restr0.109
r_bond_other_d0.033
r_gen_planes_other0.016
r_bond_refined_d0.012
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 Atoms2358
Nucleic Acid Atoms
Solvent Atoms317
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing