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Structure of Glycilhalorhodopsin from Salinarimonas soli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8 296 Li2SO4, NaCl, HEPES, PEG-200
Crystal Properties Matthews coefficient Solvent content 3.16 61.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.22 α = 90 b = 126.18 β = 104.77 c = 97.61 γ = 90
Symmetry Space Group P 1 21 1
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 4M 2022-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0520 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.63 48.06 99.92 0.175 0.184 0.057 9.4 10.1 123100 45.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.63 2.72 99.27 0.773 0.848 0.416 0.716 1.5 3.97
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.63 47.19 1.36 122930 3875 99.36 0.21 0.2088 0.2146 0.2464 0.2471 49.59
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 21.0334 f_angle_d 0.5035 f_chiral_restr 0.0358 f_plane_restr 0.0038 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11491 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 905
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building