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Dark-adapted structure of Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich at room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.5 293 100mM MES pH 5.5, 33% PEG 600, 150mM Na chloride, 150mM Ca chloride
Crystal Properties Matthews coefficient Solvent content 2.24 44.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.91 α = 90 b = 48.351 β = 90 c = 105.364 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 PIXEL DECTRIS PILATUS3 6M 2017-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96862 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 105.36 88.99 0.401 0.126 0.995 6.6 8.5 18417
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 88.13 0.138 0.623 0.316 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1UAZ 1.85 52.68 17485 970 89.18 0.1756 0.1747 0.1746 0.1917 0.1915 RANDOM 26.542
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] 1.23 -0.14 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.806 r_dihedral_angle_4_deg 23.89 r_dihedral_angle_3_deg 12.378 r_dihedral_angle_1_deg 4.569 r_angle_refined_deg 0.951 r_angle_other_deg 0.337 r_chiral_restr 0.058 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.806 r_dihedral_angle_4_deg 23.89 r_dihedral_angle_3_deg 12.378 r_dihedral_angle_1_deg 4.569 r_angle_refined_deg 0.951 r_angle_other_deg 0.337 r_chiral_restr 0.058 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1814 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 435
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction