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TEAD2 YAP binding domain (YBD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DQE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 3.1M Na Formate, 100mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.727 α = 90 b = 61.691 β = 117.26 c = 80.156 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 PIXEL DECTRIS PILATUS 6M 2021-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1 SSRL BL9-2
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 3.13 57.64 90.6 0.8 2.3 3.5 15703
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 3.2 3.4 0.2
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 3.13 57.64 1.34 9412 944 99.27 0.2505 0.2432 0.2529 0.3164 0.3144
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 8.833 f_angle_d 1.912 f_chiral_restr 0.103 f_bond_d 0.017 f_plane_restr 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2974 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement Aimless data scaling xia2 data reduction PHASER phasing