8H4R

The Crystal Structure of CDK3 and CyclinE1 Complex with Dinaciclib from Biortus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.6M MgSO4, 0.1M MES pH 6.60
Crystal Properties
Matthews coefficientSolvent content
2.7354.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.027α = 90
b = 155.027β = 90
c = 76.788γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2022-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.95372CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.7544.7599.10.9767.3427244
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)
12.752.999.10.5772.14.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.7542.37127237138598.8460.1640.16140.223435.299
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]
0.5710.2850.571-1.851
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.849
r_lrange_other14.24
r_lrange_it14.227
r_dihedral_angle_6_deg12.64
r_scangle_it10.18
r_scangle_other10.179
r_mcangle_it7.939
r_mcangle_other7.939
r_dihedral_angle_2_deg7.838
r_scbond_it6.865
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.849
r_lrange_other14.24
r_lrange_it14.227
r_dihedral_angle_6_deg12.64
r_scangle_it10.18
r_scangle_other10.179
r_mcangle_it7.939
r_mcangle_other7.939
r_dihedral_angle_2_deg7.838
r_scbond_it6.865
r_scbond_other6.864
r_dihedral_angle_1_deg5.778
r_mcbond_it5.273
r_mcbond_other5.273
r_angle_refined_deg1.129
r_angle_other_deg0.361
r_nbd_refined0.194
r_symmetry_nbd_other0.191
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.163
r_symmetry_nbd_refined0.162
r_nbd_other0.156
r_symmetry_xyhbond_nbd_refined0.13
r_symmetry_nbtor_other0.076
r_chiral_restr0.05
r_symmetry_xyhbond_nbd_other0.041
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4577
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing