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Crystal structure of the rhodopsin-mini-Go complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A4M 4A4M, 5G53 experimental model PDB 5G53 4A4M, 5G53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.1 M MES pH 5.5
10-20% PEG4000
Crystal Properties Matthews coefficient Solvent content 5.65 78.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.359 α = 90 b = 151.359 β = 90 c = 96.652 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 EIGER X 16M 2017-05-14 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-05-14 M SINGLE WAVELENGTH 3 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-05-14 M SINGLE WAVELENGTH 4 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-05-16 M SINGLE WAVELENGTH 5 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2017-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA 2 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA 3 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA 4 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA 5 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 3.02 49.544 57.99 0.368 0.06 0.9997 9.416 37.3 14856 91.8
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 3.02 3.508 8 5.087 5.172 0.93 0.8612 1.937 30.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4A4M, 5G53 3.117 49.544 1.34 14851 1479 65.58 0.2592 0.2568 0.2801 0.2783 93.4663
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3973 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing