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Crystal structure of eukaryotic heliorhodopsin Cv06 from Chromera velia strain CCMP2878
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IS6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8.2 293 1.2 M sodium potassium phosphate buffer, cryoprotection in 10% (v/v) glycerol and 2.16 M sodium potassium phosphate buffer
Crystal Properties Matthews coefficient Solvent content 2.76 55.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.892 α = 105.667 b = 77.893 β = 101.164 c = 135.987 γ = 90.016
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 2M 2022-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 2.5 42.98 91.8 0.121 0.99 4.9 2.9 82180 51.38
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 2.5 2.63 69 1.144 0.168 0.7 3.2
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 6IS6 2.6 42.98 1.96 79126 1914 85.41 0.2314 0.2304 0.2312 0.2713 0.2733 62.12
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 15.0106 f_angle_d 0.4117 f_chiral_restr 0.0364 f_plane_restr 0.0029 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16985 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 1406
Software Software Software Name Purpose XDS data reduction STARANISO data scaling MoRDa phasing PHENIX refinement