6JGM

Crystal structure of CDK2 IN complex with Inhibitor NU-6140


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QXP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.1M Tris pH 8.0, 0.1M NaCl, 20% PEG monomethyl ether 550
Crystal Properties
Matthews coefficientSolvent content
2.0439.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.491α = 90
b = 72.01β = 90
c = 72.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNonius Kappa CCDmirrors2018-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX21.0Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.353.0199.50.0989.66.612976
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3895.60.572.26.6

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 REPLACEMENTTHROUGHOUT3QXP2.351.031228365399.390.21790.213860.29036RANDOM41.699
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.143
r_dihedral_angle_3_deg18.594
r_dihedral_angle_4_deg18.233
r_long_range_B_other9.553
r_long_range_B_refined9.504
r_scangle_other6.924
r_dihedral_angle_1_deg6.613
r_mcangle_it4.345
r_scbond_other3.871
r_scbond_it3.597
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg45.143
r_dihedral_angle_3_deg18.594
r_dihedral_angle_4_deg18.233
r_long_range_B_other9.553
r_long_range_B_refined9.504
r_scangle_other6.924
r_dihedral_angle_1_deg6.613
r_mcangle_it4.345
r_scbond_other3.871
r_scbond_it3.597
r_mcbond_it2.724
r_angle_refined_deg1.728
r_angle_other_deg1.02
r_chiral_restr0.117
r_gen_planes_other0.033
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.004
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_mcbond_other
r_mcangle_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2245
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing