4E9D | pdb_00004e9d

The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with 3-(1-benzothiophen-2-yl)propanoyl-derivatized DPPLHSpTA peptide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M sodium acetate, 1.0 M LiCl, 30% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0138.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.873α = 85.84
b = 36.302β = 77.21
c = 47.474γ = 68.24
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDBruker Platinum 1352011-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR

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
12.7546.2996.2563654222

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTION3P2ZTHROUGHOUT2.7546.29508424694.570.269840.266910.26720.329840.3217RANDOM12.783
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_deg34.125
r_dihedral_angle_3_deg16.286
r_dihedral_angle_4_deg11.497
r_dihedral_angle_1_deg4.98
r_angle_refined_deg2.765
r_scangle_it0.502
r_mcbond_it0.446
r_scbond_it0.285
r_mcangle_it0.249
r_chiral_restr0.173
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.125
r_dihedral_angle_3_deg16.286
r_dihedral_angle_4_deg11.497
r_dihedral_angle_1_deg4.98
r_angle_refined_deg2.765
r_scangle_it0.502
r_mcbond_it0.446
r_scbond_it0.285
r_mcangle_it0.249
r_chiral_restr0.173
r_bond_refined_d0.026
r_gen_planes_refined0.004
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 Atoms1833
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms6

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
MOLREPphasing
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling