2V5Q

CRYSTAL STRUCTURE OF WILD-TYPE PLK-1 KINASE DOMAIN IN COMPLEX WITH A SELECTIVE DARPIN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OL5PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141
experimental modelPDB 3H10PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141
experimental modelPDB 1MJ0PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13030.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT AT 303 K.
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.329α = 90
b = 135.225β = 90
c = 136.824γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2006-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.396.299.30.0615.73.55170245.7
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)
12.32.4299.30.43.33.6

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 REPLACEMENTTHROUGHOUTPLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 1412.361.0849051260198.90.1840.1820.224RANDOM34.28
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]
1.07-1.870.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.477
r_dihedral_angle_4_deg18.875
r_dihedral_angle_3_deg15.116
r_scangle_it7.068
r_dihedral_angle_1_deg5.952
r_scbond_it5.214
r_mcangle_it2.8
r_mcbond_it1.615
r_angle_refined_deg1.265
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.477
r_dihedral_angle_4_deg18.875
r_dihedral_angle_3_deg15.116
r_scangle_it7.068
r_dihedral_angle_1_deg5.952
r_scbond_it5.214
r_mcangle_it2.8
r_mcbond_it1.615
r_angle_refined_deg1.265
r_nbtor_refined0.307
r_symmetry_vdw_refined0.207
r_nbd_refined0.199
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.144
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.004
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6502
Nucleic Acid Atoms
Solvent Atoms406
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing