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Crystal structure of human two pore domain potassium ion channel TREK-2 (K2P10.1) in complex with a nanobody (Nb58)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XDK experimental model PDB 5HVG Polyalanine, CDR3 loop and C-terminal removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10 277 0.1 M glycine pH 10.0, 0.2 M NaCl, 31% v/v polyethylene glycol 1000
Crystal Properties Matthews coefficient Solvent content 3.87 68.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 233.663 α = 90 b = 233.663 β = 90 c = 67.388 γ = 120
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 PILATUS3 6M 2017-07-02 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) 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 3.591 44.158 88.6 0.116 0.051 0.996 8.6 5.2 14181
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.591 3.691 55.7 1.339 0.649 0.511 1.3 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.588 30.84 14165 736 88.4 0.2579 0.2556 0.2564 0.2984 0.3051 RANDOM 154.17
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] 6.1122 6.1122 -12.2244
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.35 t_omega_torsion 1.94 t_angle_deg 0.71 t_bond_d 0.005 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5132 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 3
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing