6Q4F

CDK2 in complex with FragLite32


X-RAY DIFFRACTION

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
1.9737.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.187α = 90
b = 71.467β = 90
c = 72.042γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-02-19MSINGLE 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
11.2172.0499.90.040.9915.36.684174
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)
11.211.2397.70.680.3113.7

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 REPLACEMENTTHROUGHOUT1HCK1.2150.7980037413799.810.169140.167320.20515RANDOM25.927
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]
-0.85-0.381.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.431
r_rigid_bond_restr16.983
r_dihedral_angle_4_deg16.374
r_dihedral_angle_3_deg15.09
r_long_range_B_refined7.052
r_long_range_B_other7.051
r_scangle_other6.458
r_dihedral_angle_1_deg6.023
r_scbond_it5.577
r_scbond_other5.575
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.431
r_rigid_bond_restr16.983
r_dihedral_angle_4_deg16.374
r_dihedral_angle_3_deg15.09
r_long_range_B_refined7.052
r_long_range_B_other7.051
r_scangle_other6.458
r_dihedral_angle_1_deg6.023
r_scbond_it5.577
r_scbond_other5.575
r_mcangle_other4.897
r_mcangle_it4.892
r_mcbond_it3.914
r_mcbond_other3.9
r_angle_other_deg2.335
r_angle_refined_deg1.996
r_chiral_restr0.115
r_bond_other_d0.033
r_gen_planes_other0.019
r_bond_refined_d0.015
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 Atoms2366
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing