3D5V

Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MQ4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277hanging-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 HEPES pH 7.5, 0.2 M (NH4)2SO4, 25% PEG 3350, and 5% glycerol; cryoprotectant: 15% ethylene glycol., VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.8356.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 134.767α = 90
b = 134.767β = 90
c = 134.767γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180CCDADSC QUANTUM 3152006-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.98SSRLBL11-1

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
12.43099.70.0579.85.416020
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)
2.42.531000.3762

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 REPLACEMENTTHROUGHOUT1mq42.43014785122799.630.236650.233960.26897RANDOM53.555
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_deg29.487
r_dihedral_angle_4_deg13.88
r_dihedral_angle_3_deg13.736
r_dihedral_angle_1_deg4.169
r_mcangle_it2.372
r_scangle_it1.778
r_mcbond_it1.357
r_scbond_it1.038
r_angle_refined_deg0.866
r_nbtor_refined0.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.487
r_dihedral_angle_4_deg13.88
r_dihedral_angle_3_deg13.736
r_dihedral_angle_1_deg4.169
r_mcangle_it2.372
r_scangle_it1.778
r_mcbond_it1.357
r_scbond_it1.038
r_angle_refined_deg0.866
r_nbtor_refined0.294
r_nbd_refined0.161
r_symmetry_vdw_refined0.116
r_xyhbond_nbd_refined0.092
r_symmetry_hbond_refined0.075
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms2091
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing