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Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM 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 6.5 293 0.1 M GABA, 0.2 M Ca(OAc)2, 0.1 M MES buffer, 10% PEG8000
Crystal Properties Matthews coefficient Solvent content 4.27 71.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.604 α = 90 b = 146.563 β = 111.39 c = 140.242 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 100 PIXEL DECTRIS PILATUS 6M 2018-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97857 SOLEIL PROXIMA 1
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 2.58 49.35 99.7 0.068 0.077 0.035 0.999 13.4 4.8 123740 87.61
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 2.58 2.63 95.2 1.394 1.572 0.719 0.458 4.6
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 2.59 47.06 123710 6188 99.8 0.231 0.23 0.2311 0.246 0.2461 RANDOM 77.43
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] -1.9344 2.5217 9.4869 -7.5524
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.26 t_omega_torsion 2.77 t_angle_deg 0.94 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 15.26 t_omega_torsion 2.77 t_angle_deg 0.94 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 16423 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 356
Software Software Software Name Purpose BUSTER refinement MxCuBE data collection XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction