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X-ray structure of TEAD4(Y429H) mutant) complexed with YAP (wildtype): Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy
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 5.6 298 1.4M Na/K PO4
Crystal Properties Matthews coefficient Solvent content 2.29 46.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.843 α = 90 b = 58.843 β = 90 c = 159.101 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 2018-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99981 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.65 19.95 99.9 0.079 0.083 21 13 34599 27.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 100 1.01 1.05 0.88 2.6 13.5
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 1.65 19.95 32868 1730 99.91 0.2252 0.2245 0.2233 0.2373 0.2359 RANDOM 23.128
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] 0.07 0.07 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.377 r_dihedral_angle_4_deg 16.632 r_dihedral_angle_3_deg 11.639 r_dihedral_angle_1_deg 5.173 r_angle_refined_deg 1.023 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2079 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 25
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction