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Crystal structure of N2C/D282C stabilized opsin bound to RS06
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 AMMONIUM SULPHATE, SODIUM ACETATE, D(+)-TREHALOSE, PH 6.0
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 243.391 α = 90 b = 243.391 β = 90 c = 111.547 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 PILATUS 6M 2015-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.62 49.3 100 0.1991 0.1991 9.62 11.53 37925
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.62 2.72 100 1.0205 1.0205 0.66 11.92
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 4J4Q 2.62 47.647 1.33 37795 1881 99.63 0.2369 0.2361 0.2435 0.2525 0.257
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 13.637 f_angle_d 0.657 f_chiral_restr 0.038 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2591 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 205
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling