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Structure of the viral channelrhodopsin OLPVR1 at low pH obtained by soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AKY
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; Soaked: 100 mM sodium citrate pH 2.5, 900 mM NaCl, and 24% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.235 α = 90 b = 115.755 β = 90 c = 53.214 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 EIGER2 X CdTe 16M 2022-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.41 33.42 92.8 0.025 0.999 13.1 4.9 36461 24.97
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.55 75.9 0.952 0.316 0.8 6.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7AKY 1.41 33.42 1.34 36424 1781 64.55 0.1892 0.1877 0.1884 0.218 0.2175 31.74
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 15.7115 f_angle_d 0.9312 f_chiral_restr 0.0745 f_bond_d 0.0082 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1900 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 220
Software Software Software Name Purpose MxCuBE data collection XDS data reduction STARANISO data scaling PHASER phasing PHENIX refinement