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SMAD4 MH2 domain (residues 314-552) bound by Nanobody A7 (NbA7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YGS in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 Precipitant: 17 % w/v PEG 10000, 0.1 M sodium acetate and 0.1 M Bis-Tris pH 5.5; Cryo-protectant: perfluoropolyether oil
Crystal Properties Matthews coefficient Solvent content 3.33 63.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.126 α = 119.933 b = 147.899 β = 94.326 c = 148.856 γ = 89.308
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 4M 2024-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 3.04 74.22 79 0.125 0.843 2.7 2.2 28065 36.9
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 3.041 3.59 0.826
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.04 74.22 1.98 28065 1408 47.05 0.2296 0.2271 0.2295 0.2737 0.2369 52.4
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 14.5456 f_angle_d 0.7696 f_chiral_restr 0.0493 f_plane_restr 0.0062 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13915 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 99
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHASER phasing