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Crystal structure of beta-TrCP bound by diphosphorylated PDCD4 degron peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Non-public structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG10K, 0.1 M
Na-Hepes pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.83 32.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.719 α = 90 b = 46.971 β = 90 c = 150.861 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2024-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.217 75.43 91.6 0.999 9.8 7.7 84489
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.217 1.277 0.653
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.217 75.43 84489 4259 87.8 0.2136 0.2122 0.1995 0.2404 0.2279 RANDOM 18.8
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] 0.2044 -0.2303 0.0259
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.23 t_omega_torsion 5.56 t_angle_deg 1.28 t_bond_d 0.014 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2887 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms 5
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling PHASER phasing