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Crystal structure of Human Catenin Beta-1 in complex with stitched peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z6G MrBump
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 100 mM TRIS pH 8.75, 2%(w/v) PEG-6000, cryoprotected in 30% (w/v) Glucose.
Crystal Properties Matthews coefficient Solvent content 2.72 54.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.567 α = 90 b = 103.617 β = 90 c = 187.923 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 EIGER2 XE 16M 2023-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9212 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.129 93.961 94.7 0.036 0.999 11.9 13.7 51113 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.129 2.31 64.9 0.319 0.816 1.3 14.2
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.13 93.961 51110 2502 72.073 0.203 0.2011 0.2403 0.2062 48.028
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] 0.57 -0.827 0.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.213 r_lrange_other 14.577 r_lrange_it 14.558 r_dihedral_angle_3_deg 13.3 r_scangle_it 12.041 r_scangle_other 12.04 r_dihedral_angle_other_1_deg 10.5 r_mcangle_other 10.158 r_mcangle_it 10.156 r_scbond_it 8.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.213 r_lrange_other 14.577 r_lrange_it 14.558 r_dihedral_angle_3_deg 13.3 r_scangle_it 12.041 r_scangle_other 12.04 r_dihedral_angle_other_1_deg 10.5 r_mcangle_other 10.158 r_mcangle_it 10.156 r_scbond_it 8.622 r_scbond_other 8.617 r_mcbond_it 7.354 r_mcbond_other 7.345 r_dihedral_angle_1_deg 4.019 r_dihedral_angle_2_deg 3.207 r_angle_refined_deg 1.196 r_angle_other_deg 0.437 r_nbd_refined 0.197 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.144 r_nbd_other 0.139 r_ncsr_local_group_1 0.111 r_symmetry_nbd_refined 0.085 r_symmetry_nbtor_other 0.068 r_chiral_restr 0.063 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7696 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement GDA data collection DIALS data reduction STARANISO data scaling MrBUMP phasing