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Crystal structure of viral channelrhodopsin OLPVR1 in a complex with barium ion bound at the surface
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9IN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8 293 100 mM Tris, 900 mM NaCl, and 24% (w/v) PEG 6000
Soaking: 100 mM Tris, 900 mM NaCl, 24% (w/v) PEG 6000, and 100 mM BaCl2
Crystal Properties Matthews coefficient Solvent content 2.52 51.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.219 α = 90 b = 115.034 β = 90 c = 53.294 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER X 16M 2024-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.7000 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.1 26.65 99.9 0.211 0.998 6.75 6.1 32029 39.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 100 2.682 0.164 0.68 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 26.65 1.92 32011 1642 99.9 0.2093 0.2071 0.2495 45.34
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.1088 f_angle_d 0.5179 f_chiral_restr 0.0394 f_plane_restr 0.003 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1908 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 186
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement