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Ternary structure of GDF11 bound to ActRIIB-ECD and Alk5-ECD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E4G 5E4G, 3KFD, 1NYS experimental model PDB 3KFD 5E4G, 3KFD, 1NYS experimental model PDB 1NYS 5E4G, 3KFD, 1NYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 .05-.15M sodium acetate
12-24% polyethylene glycol 8000
.05-.15M sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 3.42 64.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.624 α = 90 b = 116.624 β = 90 c = 56.625 γ = 120
Symmetry Space Group P 32 1 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER X 16M 2018-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033202 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.34 50.5 99.91 0.0269 0.038 0.0269 0.999 12.07 2 18669 66.62
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 2.34 2.424 99.95 0.4022 0.5687 0.4022 0.455 1.51 2
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 THROUGHOUT 5E4G, 3KFD, 1NYS 2.34 50.5 1.43 18656 1865 99.93 0.2261 0.2217 0.2672 0.2724 73.7106
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2252 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing