3BZI

Molecular and structural basis of polo-like kinase 1 substrate recognition: Implications in centrosomal localization


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.5298100mM HEPES pH 7.5, 2M ammonium formate, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0138.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.726α = 90
b = 67.481β = 90
c = 87.888γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.979ESRFID14-4

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
12.136.8490.771337812144

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1owl2.136.84133781214462790.770.177850.174340.24579RANDOM20.739
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]
0.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.112
r_dihedral_angle_4_deg16.975
r_dihedral_angle_3_deg16.939
r_dihedral_angle_1_deg6.625
r_scangle_it4.737
r_scbond_it3.195
r_mcangle_it2.046
r_angle_refined_deg1.959
r_mcbond_it1.209
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.112
r_dihedral_angle_4_deg16.975
r_dihedral_angle_3_deg16.939
r_dihedral_angle_1_deg6.625
r_scangle_it4.737
r_scbond_it3.195
r_mcangle_it2.046
r_angle_refined_deg1.959
r_mcbond_it1.209
r_nbtor_refined0.308
r_nbd_refined0.225
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_refined0.192
r_symmetry_hbond_refined0.185
r_chiral_restr0.133
r_bond_refined_d0.022
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1865
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing