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X-ray structure of TEAD4(E263A+Y429F mutant) complexed with YAP(wildtype): The role of residual flexibility and water molecules in the adaptation of a bound intrinsically disordered protein to mutations at a binding interface
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 2M ammonium sulfate, 0.1M Bis-TRIS
Crystal Properties Matthews coefficient Solvent content 2.29 46.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.902 α = 90 b = 58.902 β = 90 c = 158.628 γ = 90
Symmetry Space Group P 41 21 2
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 2017-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99993 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 19.49 99.9 0.085 0.088 0.999 23 12.8 26774 28.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 99.9 0.812 0.845 0.919 3.8 13.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6GE3 1.8 19.49 25434 1339 99.85 0.2196 0.2186 0.2181 0.2385 0.2394 RANDOM 23
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] 0.06 0.06 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.855 r_dihedral_angle_4_deg 16.575 r_dihedral_angle_3_deg 11.279 r_dihedral_angle_1_deg 4.93 r_angle_refined_deg 0.931 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2069 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 35
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction