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Crystal structure of human TEAD2-Yap binding domain covalently bound to an allosteric regulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6E5G 6E5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Sodium Formate 1.8M - 2.4M
HEPES pH 7.2 - 7.4
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.898 α = 90 b = 61.666 β = 117.519 c = 79.766 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2020-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00003 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.26 53.56 88.1 0.125 0.146 0.076 0.994 8.8 3.7 12980 37.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.26 2.57 66.1 0.811 0.961 0.508 0.713 1.5 3.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6E5G 2.26 53.56 1.34 12974 671 52.21 0.2115 0.2086 0.2093 0.266 0.2609 41.88
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_angle_d 0.5112 f_chiral_restr 0.0392 f_bond_d 0.0032 f_plane_restr 0.003 f_dihedral_angle_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3360 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 51
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing