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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 30% PEG 8000, 0.1 M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.13 42.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.837 α = 90 b = 70.059 β = 90 c = 87.182 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 PIXEL DECTRIS PILATUS3 6M 2009-05-20 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 1.6 34.59 99.7 0.0038 23.6 4.8 46555
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 1.6 1.64 0.08
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 1.6 34.59 44227 2328 99.75 0.1771 0.1746 0.1822 0.2228 0.2304 RANDOM 30.011
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] -0.27 0.36 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.909 r_dihedral_angle_4_deg 15.831 r_dihedral_angle_3_deg 13.422 r_dihedral_angle_1_deg 8.003 r_angle_other_deg 1.044 r_angle_refined_deg 0.999 r_rigid_bond_restr 0.51 r_chiral_restr 0.023 r_gen_planes_refined 0.009 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.909 r_dihedral_angle_4_deg 15.831 r_dihedral_angle_3_deg 13.422 r_dihedral_angle_1_deg 8.003 r_angle_other_deg 1.044 r_angle_refined_deg 0.999 r_rigid_bond_restr 0.51 r_chiral_restr 0.023 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_bond_refined_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2684 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 100
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing