6Q49

CDK2 in complex with FragLite6


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
1.9938.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.069α = 90
b = 72.53β = 90
c = 71.899γ = 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
1172.5399.90.050.9911.46.6149763
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)
111.0299.31.910.280.64.3

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 REPLACEMENTTHROUGHOUT1HCK142.87142358740599.870.176290.175240.19718RANDOM23.835
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]
0.110.09-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.941
r_rigid_bond_restr25.357
r_mcbond_other16.576
r_mcbond_it16.569
r_mcangle_it16.007
r_mcangle_other16.001
r_long_range_B_refined15.752
r_long_range_B_other15.749
r_dihedral_angle_3_deg14.768
r_dihedral_angle_4_deg14.684
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.941
r_rigid_bond_restr25.357
r_mcbond_other16.576
r_mcbond_it16.569
r_mcangle_it16.007
r_mcangle_other16.001
r_long_range_B_refined15.752
r_long_range_B_other15.749
r_dihedral_angle_3_deg14.768
r_dihedral_angle_4_deg14.684
r_scangle_other14.673
r_scbond_it11.907
r_scbond_other11.902
r_dihedral_angle_1_deg6.031
r_angle_other_deg2.317
r_angle_refined_deg2.15
r_chiral_restr0.136
r_bond_other_d0.033
r_gen_planes_other0.027
r_bond_refined_d0.018
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 Atoms2307
Nucleic Acid Atoms
Solvent Atoms305
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing