5ETZ

Structure of the all-trans isomer of pharaonis halorhodopsin in the absence of halide ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QBG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6288The 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 coefficientSolvent content
3.2261.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.4α = 90
b = 97.77β = 128.81
c = 101.62γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11SPring-8BL38B1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.850.7791.30.0650.06512.73.599234992342.516
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.960.90.4052.72.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3qbg1.81599008500191.20.21850.2357Random 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]
0.470.9192.01-2.48
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5900
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms343

Software

Software
Software NamePurpose
CNSrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
XTALVIEWmodel building