3ABW

Crystal structure of pharaonis halorhodopsin in complex with azide ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A7KPDB ENTRY 3a7k

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6288A DROP CONTAINING 2MG/ML Halorhodopsin, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M Na-citrate, 0.04% NAN3,5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSIONAGAINST A RESERVE SOLUTION CONTAINING 2.9 M AMMONIUM SULFATE, 0.04M Na-citrate, PH 6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 288K. After the crystal grew, the mother solution was exchanged with a solution containing 3M Ammonium sulfate, 200 mM Na-N3, 100 mM HEPES (pH7) and 30 % trehalose.
Crystal Properties
Matthews coefficientSolvent content
3.261.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.09α = 90
b = 98.79β = 127.85
c = 100.14γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirrors2009-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0SPring-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
11.938.15880.0710.07110.53.2917958079923.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.9274.30.5260.5262.23

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3a7k1.9159182180687406487.90.24230.2626RANDOM32.4952
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]
2.914-9.532-1.368-1.546
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.434
c_scbond_it1.816
c_mcangle_it1.809
c_mcbond_it1.239
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5889
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms303

Software

Software
Software NamePurpose
MAR345dtbdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing