2B54

Human cyclin dependent kinase 2 (CKD2)complexed with DIN-232305


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4291100mM HEPES pH 7.4, 50mM Ammonium Acetate, 2mM DTT, 4-14% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1342.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.97α = 90
b = 73.16β = 90
c = 54.26γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATERIGAKU RAXIS II1997-10-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.8437.4483.70.0993.12.2217799.8
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)
1.841.8767.30.4570.51.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIN-HOUSE CDK2 MODEL1.8537.44220039838780.1580.263RANDOM29
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]
-1.162.65-1.49
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d30.2
c_scbond_it14
c_scangle_it13.87
c_angle_deg9.5
c_improper_angle_d8.27
c_mcangle_it3.25
c_mcbond_it1.89
c_bond_d0.154
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d30.2
c_scbond_it14
c_scangle_it13.87
c_angle_deg9.5
c_improper_angle_d8.27
c_mcangle_it3.25
c_mcbond_it1.89
c_bond_d0.154
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2911
Nucleic Acid Atoms
Solvent Atoms318
Heterogen Atoms30

Software

Software
Software NamePurpose
PROCESSdata collection
SCALEdata reduction
X-PLORmodel building
CNXrefinement
PROCESSdata reduction
SCALEdata scaling
X-PLORphasing