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Structure of human PLK1 in complex with 2-Allyl-1-[6-(1-hydroxy-1-methyl-ethyl)-pyridin-2-yl]-6-[4-(4-methyl-piperazin-1-yl)-phenylamino]-1,2-dihydro-pyrazolo[3,4-d]pyrimidin-3-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RKU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 16% w/v PEG4000, 0.1 M Na citrate pH 6.50, 0.6 M Mg acetate, 0.0003 M Zn acetate
Crystal Properties Matthews coefficient Solvent content 2.96 58.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.932 α = 90 b = 66.932 β = 90 c = 154.963 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99991 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.188 54.29 83.3 0.053 0.029 0.999 11.8 2.9 7568
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.188 2.507 0.69 0.312 0.816 2 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2rku 2.188 54.29 7568 399 35.2 0.2032 0.2002 0.2061 0.2547 0.2325 RANDOM 50.82
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] 1.2438 1.2438 -2.4876
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.54 t_omega_torsion 2.76 t_angle_deg 1 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.54 t_omega_torsion 2.76 t_angle_deg 1 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2365 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 42
Software Software Software Name Purpose BUSTER refinement XDS data scaling XDS data reduction PHASER phasing