6Q4H

CDK2 in complex with FragLite36


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
1.9938.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.152α = 90
b = 72.219β = 90
c = 71.932γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-04-15MSINGLE 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
1172.2298.90.070.9910.26147934
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)
111.0286.20.580.571.12.9

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 REPLACEMENTTHROUGHOUT1HCK142.84140569736598.890.191750.190980.20663RANDOM18.136
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]
1.41-0.1-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.755
r_rigid_bond_restr24.956
r_dihedral_angle_3_deg14.809
r_dihedral_angle_4_deg13.288
r_long_range_B_refined8.901
r_long_range_B_other8.899
r_scbond_it8.295
r_scbond_other8.293
r_mcangle_it8.136
r_mcangle_other8.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.755
r_rigid_bond_restr24.956
r_dihedral_angle_3_deg14.809
r_dihedral_angle_4_deg13.288
r_long_range_B_refined8.901
r_long_range_B_other8.899
r_scbond_it8.295
r_scbond_other8.293
r_mcangle_it8.136
r_mcangle_other8.134
r_scangle_other7.942
r_mcbond_it6.807
r_mcbond_other6.807
r_dihedral_angle_1_deg5.338
r_angle_other_deg2.311
r_angle_refined_deg2.005
r_chiral_restr0.121
r_bond_other_d0.034
r_bond_refined_d0.017
r_gen_planes_other0.016
r_gen_planes_refined0.012
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 Atoms2350
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing