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Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.5 M ammonium sulphate, 12% glycerol, 0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 3.72 66.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.345 α = 90 b = 89.345 β = 90 c = 131.659 γ = 120
Symmetry Space Group P 64 2 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 PILATUS3 6M 2009-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.76 33.35 99.9 0.0142 21.4 12.6 8495
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.76 2.83 0.0826 4.1
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 2F0A 2.76 33.35 8069 425 99.87 0.2465 0.2444 0.2428 0.2848 0.2832 RANDOM 43.802
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] 1.02 0.51 1.02 -3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.938 r_dihedral_angle_4_deg 19.074 r_dihedral_angle_3_deg 16.938 r_dihedral_angle_1_deg 4.897 r_angle_other_deg 1.204 r_angle_refined_deg 1.083 r_rigid_bond_restr 0.31 r_chiral_restr 0.038 r_gen_planes_refined 0.007 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.938 r_dihedral_angle_4_deg 19.074 r_dihedral_angle_3_deg 16.938 r_dihedral_angle_1_deg 4.897 r_angle_other_deg 1.204 r_angle_refined_deg 1.083 r_rigid_bond_restr 0.31 r_chiral_restr 0.038 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1320 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 68
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing