3A7K

Crystal structure of halorhodopsin from Natronomonas pharaonis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E12PDB ENTRY 1e12

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293A DROP CONTAINING 1MG/ML PROTEIN, 1M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, 0.04% NAN2, 5MG/ML NONYL GLUCOSIDE WAS CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVE SOLUTION CONTAINING 2.6 M AMMONIUM SULFATE, 0.16M NACL, 0.04M TRIS-HCL, PH 8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Crystal Properties
Matthews coefficientSolvent content
3.261.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.83α = 90
b = 99.77β = 127.67
c = 99.27γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2009-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

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
1260.199.50.0720.0729.92.77909231.2
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)
22.111000.5560.55622.7

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 1e122157892578528397599.60.2490.274RANDOM49.222
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]
2.094-12.7482.659-4.754
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.394
c_mcangle_it1.895
c_scbond_it1.717
c_mcbond_it1.28
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5868
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms666

Software

Software
Software NamePurpose
ADSCdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing