3P36

Polo-like kinase I Polo-box domain in complex with DPPLHSpTA phosphopeptide from PBIP1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UMW1UMW (chain A)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.2293100mM Na/K phosphate, 0.2M NaCl, 10% PEG 8000, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9536.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.931α = 90
b = 50.116β = 99.31
c = 58.73γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2010-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

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
11.5957.9399.42777427603

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 REPLACEMENTTHROUGHOUT1UMW (chain A)1.5957.9326218138599.40.197570.194650.25237RANDOM22.027
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_deg34.697
r_dihedral_angle_4_deg24.866
r_dihedral_angle_3_deg16.381
r_dihedral_angle_1_deg6.825
r_scangle_it5.052
r_scbond_it3.511
r_mcangle_it2.514
r_angle_refined_deg2.255
r_mcbond_it1.519
r_chiral_restr0.193
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.697
r_dihedral_angle_4_deg24.866
r_dihedral_angle_3_deg16.381
r_dihedral_angle_1_deg6.825
r_scangle_it5.052
r_scbond_it3.511
r_mcangle_it2.514
r_angle_refined_deg2.255
r_mcbond_it1.519
r_chiral_restr0.193
r_bond_refined_d0.025
r_gen_planes_refined0.012
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms1804
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms11

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement