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Structure of the pentameric ligand-gated ion channel ELIC in complex with a NAM nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VL0 2vl0, 3p0g experimental model PDB 3P0G 2vl0, 3p0g
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M Na2SO4, 0.1 M bis-trispropane, 10% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.99 69.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.804 α = 71.02 b = 122.354 β = 64.19 c = 128.221 γ = 61.66
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 2M-F 2011-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.25 48.32 89.8 0.053 0.074 0.053 0.993 5.6 1.8 82177 105.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.25 3.42 60.3 0.807 1.141 0.807 0.483 1.7
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 2vl0, 3p0g 3.25 48.32 82174 4085 89.9 0.249 0.248 0.2629 0.264 0.2684 RANDOM 104.73
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] -2.3709 1.5816 3.2684 2.4382 0.8879 -0.0673
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.29 t_omega_torsion 2.42 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.29 t_omega_torsion 2.42 t_angle_deg 0.97 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 25905 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 328
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing PHENIX refinement BUSTER refinement PDB_EXTRACT data extraction