6Q3C

CDK2 in complex with FragLite1


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
1.9737.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.439α = 90
b = 71.333β = 90
c = 71.886γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.919DiamondI24

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
11.2950.6388.50.130.998.36.661548
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.291.3146.10.431.54.5

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 REPLACEMENTTHROUGHOUT1HCK1.2950.6358568298088.140.142370.14050.17813RANDOM25.147
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]
-0.460.77-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.647
r_dihedral_angle_3_deg15.474
r_dihedral_angle_4_deg15.263
r_rigid_bond_restr13.289
r_long_range_B_refined6.879
r_long_range_B_other6.878
r_dihedral_angle_1_deg6.108
r_scangle_other5.846
r_mcangle_it4.863
r_mcangle_other4.863
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.647
r_dihedral_angle_3_deg15.474
r_dihedral_angle_4_deg15.263
r_rigid_bond_restr13.289
r_long_range_B_refined6.879
r_long_range_B_other6.878
r_dihedral_angle_1_deg6.108
r_scangle_other5.846
r_mcangle_it4.863
r_mcangle_other4.863
r_scbond_it4.841
r_scbond_other4.839
r_mcbond_it4.674
r_mcbond_other4.669
r_angle_other_deg2.301
r_angle_refined_deg1.755
r_chiral_restr0.1
r_bond_other_d0.033
r_gen_planes_other0.016
r_bond_refined_d0.012
r_gen_planes_refined0.011
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 Atoms2334
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing