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Structure of PLK1 in complex with peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UMW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 2M Ammonium sulfate, 100mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.36 47.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.114 α = 90 b = 69.248 β = 98.63 c = 56.513 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU SATURN 944+ 2013-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-002+ 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 24.53 99.5 24869 24743 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 99.5 0.038 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1UMW 1.8 24.53 24869 23483 1259 99.44 0.14292 0.1398 0.1515 0.2013 0.2065 RANDOM 15.933
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] 0.2 0.19 -0.61 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.184 r_dihedral_angle_4_deg 19.691 r_sphericity_free 17 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_1_deg 5.895 r_sphericity_bonded 5.892 r_rigid_bond_restr 3.758 r_angle_refined_deg 2.194 r_angle_other_deg 1.004 r_chiral_restr 0.169
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.184 r_dihedral_angle_4_deg 19.691 r_sphericity_free 17 r_dihedral_angle_3_deg 14.925 r_dihedral_angle_1_deg 5.895 r_sphericity_bonded 5.892 r_rigid_bond_restr 3.758 r_angle_refined_deg 2.194 r_angle_other_deg 1.004 r_chiral_restr 0.169 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2018 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 15
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling