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3.0A SYN structure of the multi-domain human smoothened receptor in complex with TC114
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V56
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5 293 100 mM Sodium citrate tribasic dihydrate pH 5.0, 36% (v/v) PEG 400, 50-200 mM Ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 2.85 56.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.08 α = 90 b = 356.36 β = 102.79 c = 59.09 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 77 PIXEL DECTRIS PILATUS3 6M 2015-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 3 48.38 91.9 0.117 7.5 3.7 29571 72.64
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 3 3.16 81.3 0.393 1.9 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 5V56 3 48.38 29552 1502 91.9 0.205 0.203 0.2228 0.24 0.2585 RANDOM 82.72
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] 4.083 -0.1952 4.3715 -8.4546
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 2.76 t_other_torsion 1.98 t_angle_deg 0.93 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_omega_torsion 2.76 t_other_torsion 1.98 t_angle_deg 0.93 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 9949 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 152
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling PHASER phasing