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Crystal structure of human Brachyury G177D variant in complex with SJF-4601
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG3350 12%, 0.2 M NaSCN, 5 mM Betaine
Crystal Properties Matthews coefficient Solvent content 1.92 35.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.892 α = 90 b = 70.294 β = 90 c = 81.874 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 2021-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 1.1 APS 24-ID-E
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 2.03 45.14 98.39 0.977 10.5 6.1 22141 31.2
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 2.03 2.1 0.74
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 2.03 45.14 1.38 22136 1119 98.4 0.2028 0.1996 0.1994 0.2664 0.2656
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 7.326 f_angle_d 0.641 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2773 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing