7QHL

Crystal structure of Cyclin-dependent kinase 2/cyclin A in complex with 3,5,7-Substituted pyrazolo[4,3-d]pyrimidine inhibitor 24


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7B7S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5291.1570%: 10% w/v PEG 4,000, 20% v/v glycerol, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.1 M Tris/Bicine pH 8.5 30%:20% w/v PEG 6000, 0.1 M Bicine, pH 9
Crystal Properties
Matthews coefficientSolvent content
3.1560.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.89α = 90
b = 163.9β = 106.61
c = 73.17γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.746.9697.30.1720.1850.99810.777.02316853130.849
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.895.31.9742.1360.4820.976.778

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 REPLACEMENTTHROUGHOUT7B7S1.746.96166428210097.410.20040.20010.2236RANDOM31.558
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.758
r_dihedral_angle_4_deg16.433
r_dihedral_angle_3_deg13.619
r_dihedral_angle_1_deg5.894
r_angle_other_deg2.262
r_angle_refined_deg1.571
r_chiral_restr0.084
r_bond_other_d0.033
r_bond_refined_d0.017
r_gen_planes_other0.013
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.758
r_dihedral_angle_4_deg16.433
r_dihedral_angle_3_deg13.619
r_dihedral_angle_1_deg5.894
r_angle_other_deg2.262
r_angle_refined_deg1.571
r_chiral_restr0.084
r_bond_other_d0.033
r_bond_refined_d0.017
r_gen_planes_other0.013
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8761
Nucleic Acid Atoms
Solvent Atoms969
Heterogen Atoms135

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction