3D5W

Crystal structure of a phosphorylated Polo-like kinase 1 (Plk1) catalytic domain in complex with ADP.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D5V 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277hanging-drop vapor diffusion at 4 C (277K); protein at 6 mg/ml in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 3 mM DTT, 4 mM ATP, and 4 mM MgSO4; crystallization condition: 0.2 M disodium tartrate dihydrate and 20% PEG 3350; cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.7955.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.99α = 90
b = 133.99β = 90
c = 133.99γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray180CCDMARMOSAIC 325 mm CCD2006-12-06MSINGLE 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
12.63099.90.0539612461
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)
2.62.7499.90.3482.2

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 REPLACEMENTTHROUGHOUT3d5v2.63011348111399.890.244180.241550.2711RANDOM61.518
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_deg32.795
r_dihedral_angle_3_deg15.017
r_dihedral_angle_4_deg14.889
r_dihedral_angle_1_deg3.954
r_mcangle_it2.098
r_scangle_it1.446
r_mcbond_it1.187
r_angle_refined_deg0.927
r_scbond_it0.875
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.795
r_dihedral_angle_3_deg15.017
r_dihedral_angle_4_deg14.889
r_dihedral_angle_1_deg3.954
r_mcangle_it2.098
r_scangle_it1.446
r_mcbond_it1.187
r_angle_refined_deg0.927
r_scbond_it0.875
r_nbtor_refined0.293
r_symmetry_vdw_refined0.167
r_nbd_refined0.162
r_xyhbond_nbd_refined0.099
r_symmetry_hbond_refined0.097
r_chiral_restr0.058
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 Atoms2264
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms27

Software

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