3T6E

Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC 19567) substrain-94


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3T6DPDB entry 3T6D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6292Protein in 20 mM sodium phosphate buffer and 0.1% lauryldimethylamine N,N-oxide (LDAO) detergent, precipitant 1.5 M ammonium sulfate, amphiphile 3% heptanetriol, reservoir solution 2.2-2.4 M ammonium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 221.583α = 90
b = 221.583β = 90
c = 113.418γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMirrors2010-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9194DiamondI02

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
11.9243.4699.50.1150.1199.419.3521213421213436
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)
11.921.9999.10.8230.8431.618.8720895

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-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3T6D1.9243.462118442012061063899.390.155980.155980.154830.17804RANDOM46.86
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]
-0.01-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.715
r_dihedral_angle_4_deg17.873
r_dihedral_angle_3_deg13.142
r_dihedral_angle_1_deg5.832
r_angle_refined_deg2.23
r_angle_other_deg1.021
r_chiral_restr0.11
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.715
r_dihedral_angle_4_deg17.873
r_dihedral_angle_3_deg13.142
r_dihedral_angle_1_deg5.832
r_angle_refined_deg2.23
r_angle_other_deg1.021
r_chiral_restr0.11
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9340
Nucleic Acid Atoms
Solvent Atoms974
Heterogen Atoms1586

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling