5FP5

Structure of cyclin-dependent kinase 2 with small-molecule ligand 4- fluorobenzoic acid (AT222) in an alternate binding site.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.410MM HEPES/NAOH PH7.4 15MM NACL PROTEIN CONCENTRATION: 8.6 MG/ML
Crystal Properties
Matthews coefficientSolvent content
2.3547

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.677α = 90
b = 71.698β = 90
c = 72.382γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC CCD2002-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRSSRS

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.163093.114466-3.732.2

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 1HCK2.1630.011446673193.120.18980.18660.253RANDOM32.09
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]
-1.84042.6526-0.8121
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.01
t_omega_torsion5.87
t_angle_deg1.04
t_bond_d0.011
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion18.01
t_omega_torsion5.87
t_angle_deg1.04
t_bond_d0.011
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2076
Nucleic Acid Atoms
Solvent Atoms321
Heterogen Atoms23

Software

Software
Software NamePurpose
BUSTERrefinement
d*TREKdata reduction
DTSCALEdata scaling
AMoREphasing