3DBD

Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain in complex with Compound 094


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.6277hanging-drop vapor diffusion at 4 C (277K); protein at 7 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl and 3 mM DTT; crystallization condition: 0.1 M tri-sodium citrate pH 5.6, 0.2 M (NH4)2SO4, and 25% PEG 3350; cryoprotectant: 15% ethylene glycol., VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.8757.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.267α = 90
b = 135.267β = 90
c = 135.267γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray160CCDADSC QUANTUM 3152007-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.98SSRLBL9-1

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
13.053099.70.0738.53.57979
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)
3.053.211000.3642.1

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 REPLACEMENTTHROUGHOUT3d5w3.0530720177899.650.252330.249690.27565RANDOM58.728
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_deg30.067
r_dihedral_angle_3_deg14.065
r_dihedral_angle_4_deg9.132
r_dihedral_angle_1_deg3.875
r_mcangle_it1.321
r_angle_refined_deg1.005
r_mcbond_it0.728
r_scangle_it0.434
r_nbtor_refined0.292
r_scbond_it0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.067
r_dihedral_angle_3_deg14.065
r_dihedral_angle_4_deg9.132
r_dihedral_angle_1_deg3.875
r_mcangle_it1.321
r_angle_refined_deg1.005
r_mcbond_it0.728
r_scangle_it0.434
r_nbtor_refined0.292
r_scbond_it0.24
r_nbd_refined0.158
r_xyhbond_nbd_refined0.128
r_symmetry_vdw_refined0.114
r_symmetry_hbond_refined0.067
r_chiral_restr0.049
r_bond_refined_d0.006
r_gen_planes_refined0.001
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2081
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing