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Crystal structure of human two pore domain potassium ion channel TREK-2 (K2P10.1) in complex with an activatory nanobody (Nb76)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BW5 experimental model PDB 5HVG Polyalanine, CDR3 and C-terminal removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1 M HEPES pH 7.0, 0.3 M BaCl2, 39% polyethylene glycol 400
Crystal Properties Matthews coefficient Solvent content 3.74 67.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.28 α = 90 b = 75.576 β = 90 c = 259.15 γ = 90
Symmetry Space Group P 21 21 21
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 0.9687 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 3.203 51.83 77.9 0.134 0.066 0.998 8.4 4 17904
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 3.203 3.336 34.4 1.065 0.522 0.615 1.7 4
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 3.2 31.11 17829 894 77.8 0.2718 0.2704 0.2669 0.2984 0.2904 RANDOM 77.01
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] -2.5586 -4.3165 6.8751
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.71 t_omega_torsion 1.98 t_angle_deg 0.65 t_bond_d 0.004 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 5321 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 144
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling STARANISO data scaling PHASER phasing