6Q3F

CDK2 in complex with FragLite2


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
1.9737.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.33α = 90
b = 71.36β = 90
c = 72.01γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.98DiamondI03

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
11.1850.7499.90.020.9914.71.990732
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)
11.181.299.50.660.471.31.9

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 REPLACEMENTTHROUGHOUT1HCK1.1850.7486255447799.80.162760.16130.18857RANDOM25.539
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]
-1.90.171.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.937
r_rigid_bond_restr23.278
r_dihedral_angle_4_deg17.516
r_dihedral_angle_3_deg14.676
r_mcangle_other13.695
r_mcangle_it13.529
r_mcbond_it10.82
r_mcbond_other10.28
r_scangle_other10.205
r_long_range_B_refined10.178
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.937
r_rigid_bond_restr23.278
r_dihedral_angle_4_deg17.516
r_dihedral_angle_3_deg14.676
r_mcangle_other13.695
r_mcangle_it13.529
r_mcbond_it10.82
r_mcbond_other10.28
r_scangle_other10.205
r_long_range_B_refined10.178
r_long_range_B_other10.176
r_scbond_it7.89
r_scbond_other7.887
r_dihedral_angle_1_deg5.617
r_angle_other_deg2.365
r_angle_refined_deg2.154
r_chiral_restr0.126
r_bond_other_d0.033
r_gen_planes_other0.026
r_bond_refined_d0.017
r_gen_planes_refined0.014
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 Atoms2364
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing