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Structure of human Smoothened in complex with cholesterol and SAG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5L7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6 293 0.1 M MES pH6.0,
0.09-0.12 M potassium formate,
24-27% (v/v) PEG500 DME,
0.5 mM zinc chloride,
0.1 M ammonium fluoride
Crystal Properties Matthews coefficient Solvent content 2.83 56.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.86 α = 90 b = 63.15 β = 96.29 c = 208.06 γ = 90
Symmetry Space Group C 1 2 1
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 2016-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 3 60.4 97.1 0.097 0.082 0.992 9.9 3.1 31218
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.08 87.5 0.797 0.796 0.363 1 2.3
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 5L7D 3 60 29738 1480 96.95 0.2331 0.2309 0.2315 0.2748 0.2698 RANDOM 130.621
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] -3.35 4.81 4.6 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.987 r_dihedral_angle_3_deg 16.819 r_dihedral_angle_4_deg 15.624 r_dihedral_angle_1_deg 5.828 r_angle_refined_deg 1.641 r_angle_other_deg 1.422 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.987 r_dihedral_angle_3_deg 16.819 r_dihedral_angle_4_deg 15.624 r_dihedral_angle_1_deg 5.828 r_angle_refined_deg 1.641 r_angle_other_deg 1.422 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9245 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling PHASER phasing