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Crystal structure of TEAD3 YAP binding domain with compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZJQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 300 0.1M HEPES pH 7.5, 0.2M Ammonium acetate, 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.17 α = 90 b = 101.74 β = 90 c = 149.08 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 CCD ADSC QUANTUM 315r 2022-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 28.17 99.82 0.03486 0.999 15.12 2 22344 53.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.693 0.3577 0.806 2.07
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 2.6 28.17 1.35 22340 1118 99.93 0.2148 0.2119 0.212 0.2702 0.271 53.16
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 16.9118 f_angle_d 1.3342 f_chiral_restr 0.064 f_bond_d 0.0103 f_plane_restr 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5268 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling ELVES phasing