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2.9A XFEL structure of the multi-domain human smoothened receptor (with E194M mutation) in complex with TC114
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C79 4C79, 4QIM, 1I1O experimental model PDB 4QIM 4C79, 4QIM, 1I1O experimental model PDB 1I1O 4C79, 4QIM, 1I1O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 100 mM Sodium citrate tribasic dihydrate pH 5.0, 36% (v/v) PEG400, 50-200 mM Ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.96 58.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.59 α = 90 b = 349.54 β = 101.1 c = 61.76 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL CS-PAD CXI-1 K-B mirrors 2016-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.3 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.9 24.9 100 0.133 5.4 366 37101 82.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 100 2.8 0.4 64.5
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 4C79, 4QIM, 1I1O 2.9 24.9 37045 1810 100 0.219 0.218 0.2543 0.239 0.2752 RANDOM 117.29
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] 18.2748 -10.6173 31.6273 -49.9021
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.31 t_omega_torsion 2.41 t_angle_deg 1.03 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.31 t_omega_torsion 2.41 t_angle_deg 1.03 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9747 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 154
Software Software Software Name Purpose BUSTER refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing