3NS9

Crystal structure of CDK2 in complex with inhibitor BS-194


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HCKPDB entry 1HCK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.82770.1M ammonium acetate, pH 7.8, 6% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
1.9938.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.05α = 90
b = 70.69β = 90
c = 72.11γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.7842.43199.40.0956.73.32636426364
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.781.8899.60.6990.69913.33774

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 REPLACEMENTTHROUGHOUTPDB entry 1HCK1.7842.4326316131199.150.20520.20210.2648RANDOM29.9882
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]
0.081.04-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.652
r_dihedral_angle_3_deg17.083
r_dihedral_angle_4_deg14.056
r_dihedral_angle_1_deg5.92
r_scangle_it5.364
r_scbond_it3.541
r_mcangle_it2.268
r_angle_refined_deg2.028
r_mcbond_it1.38
r_chiral_restr0.163
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.652
r_dihedral_angle_3_deg17.083
r_dihedral_angle_4_deg14.056
r_dihedral_angle_1_deg5.92
r_scangle_it5.364
r_scbond_it3.541
r_mcangle_it2.268
r_angle_refined_deg2.028
r_mcbond_it1.38
r_chiral_restr0.163
r_bond_refined_d0.025
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2322
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms28

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction