6Q4G

CDK2 in complex with FragLite37


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
1.9837.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.057α = 90
b = 72.244β = 90
c = 71.824γ = 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
10.9871.8298.20.090.9910.35.97698
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)
10.98178.20.590.510.92.2

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 REPLACEMENTTHROUGHOUT1HCK0.9842.8147680769898.110.191420.190430.21062RANDOM14.584
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]
-0.230.77-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.135
r_dihedral_angle_3_deg14.326
r_rigid_bond_restr12.81
r_dihedral_angle_4_deg12.345
r_dihedral_angle_1_deg5.243
r_scangle_other3.818
r_scbond_other3.569
r_scbond_it3.568
r_long_range_B_refined3.228
r_long_range_B_other3.227
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.135
r_dihedral_angle_3_deg14.326
r_rigid_bond_restr12.81
r_dihedral_angle_4_deg12.345
r_dihedral_angle_1_deg5.243
r_scangle_other3.818
r_scbond_other3.569
r_scbond_it3.568
r_long_range_B_refined3.228
r_long_range_B_other3.227
r_mcangle_it2.418
r_mcangle_other2.417
r_angle_other_deg2.342
r_mcbond_it2.134
r_mcbond_other2.13
r_angle_refined_deg2.12
r_chiral_restr0.13
r_bond_other_d0.034
r_gen_planes_other0.021
r_bond_refined_d0.019
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 Atoms2271
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing