6Q4B

CDK2 in complex with FragLite13


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
238.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.201α = 90
b = 72.191β = 90
c = 72.374γ = 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
11.1251.1199.80.030.9910.41.9107278
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)
11.121.1495.21.910.220.51.9

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 REPLACEMENTTHROUGHOUT1HCK1.1251.11101949532999.620.174240.172720.20326RANDOM22.825
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]
0.060.04-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.311
r_rigid_bond_restr21.412
r_dihedral_angle_4_deg16.749
r_dihedral_angle_3_deg14.597
r_mcbond_it7.419
r_mcbond_other7.403
r_long_range_B_refined6.767
r_long_range_B_other6.766
r_mcangle_it6.578
r_mcangle_other6.577
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.311
r_rigid_bond_restr21.412
r_dihedral_angle_4_deg16.749
r_dihedral_angle_3_deg14.597
r_mcbond_it7.419
r_mcbond_other7.403
r_long_range_B_refined6.767
r_long_range_B_other6.766
r_mcangle_it6.578
r_mcangle_other6.577
r_scangle_other6.068
r_dihedral_angle_1_deg5.926
r_scbond_it5.235
r_scbond_other5.235
r_angle_other_deg2.344
r_angle_refined_deg2.039
r_chiral_restr0.126
r_bond_other_d0.033
r_gen_planes_other0.023
r_bond_refined_d0.016
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 Atoms2347
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms7

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing