6GE6

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GE3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52982M ammonium sulfate, 0.1M Bis-TRIS
Crystal Properties
Matthews coefficientSolvent content
2.2946.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.902α = 90
b = 58.902β = 90
c = 158.628γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.99993SLSX10SA

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.819.4999.90.0850.0880.9992312.82677428.3
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)RedundancyNumber Unique Reflections (All)
11.81.8599.90.8120.8450.9193.813.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6GE31.819.4925434133999.850.21960.21860.2385RANDOM23
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]
0.060.06-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.855
r_dihedral_angle_4_deg16.575
r_dihedral_angle_3_deg11.279
r_dihedral_angle_1_deg4.93
r_angle_refined_deg0.931
r_chiral_restr0.062
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2069
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms35

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction