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Plk-1 polo-box domain in complex with histidine N(tau)-cyclized Macrocycle 5b.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 Well solution: 0.2 M Calcium Chloride, 12.5% PEG-3350
Protein: 10 mg/ml PBD-macrocycle complex in 0.5 M Sodium Chloride, 10 mM TRIS pH 8.0, 0.4 M ammonium acetate
1:1 mix of protein complex and well solution
Crystal Properties Matthews coefficient Solvent content 1.9 35.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.449 α = 90 b = 51.294 β = 100.84 c = 58.034 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 ADSC QUANTUM 315 2016-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97917 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.45 17.408 99.4 0.066 0.073 0.031 8.6 5.4 36144 15.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 99.1 0.628 0.709 0.326 0.769 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4dfw 1.45 17.408 1.37 36127 2000 99.27 0.1338 0.1319 0.1656 0.1717 23.217
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 Key Refinement Restraint Deviation f_dihedral_angle_d 16.284 f_angle_d 1.048 f_chiral_restr 0.08 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1800 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 137
Software Software Software Name Purpose ADSC data collection HKL-2000 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction