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Structure of the all-trans isomer of pharaonis halorhodopsin in the absence of halide ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 288 The crystal was prepared by the membrane fusion method. A mixture solution containing 3 mg/ml halorhodopsin, 9 mg/ml nonylglucoside, 1 M ammonium sulfate, 0.1 M sodium azide was concentrated by the sitting-drop vapor diffusion method. The crystal soaking in a halide-ion-free solution was performed under dim red light, and then the crystal was rapidly cooled with liquid propane at 87 K.
Crystal Properties Matthews coefficient Solvent content 3.22 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.4 α = 90 b = 97.77 β = 128.81 c = 101.62 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2015-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
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 1.8 50.77 91.3 0.065 0.065 12.7 3.5 99234 99234 2.5 16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 60.9 0.405 2.7 2.9
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3qbg 1.8 15 99008 5001 91.2 0.2185 0.2187 0.2357 0.235 Random selection
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] 0.47 0.919 2.01 -2.48
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5900 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 343
Software Software Software Name Purpose CNS refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing XTALVIEW model building