3D38

Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I5NPDB entry 2I5N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Plug-based Microfluidics62969 mg/mL Protein, 4.6 mM LDAO, 10 mM Methyl-beta-cyclodextrin, 1.6-1.7 M Sulfate, 4.5% w/v Triethylammonium phosphate pH 6.0, 3% 1,2,3-heptanetriol, 30 mM NaH2PO4-Na2HPO4 pH 6.0, Plug-based Microfluidics, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
7.1982.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 241.171α = 90
b = 241.171β = 90
c = 113.391γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-04-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.0332APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.25099.80.16830.366203762037

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2I5N3.215062025314599.580.1940.1920.224RANDOM67.435
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]
3.881.943.88-5.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.642
r_dihedral_angle_3_deg17.749
r_dihedral_angle_4_deg15.265
r_dihedral_angle_1_deg5.634
r_scangle_it2.275
r_angle_refined_deg1.437
r_scbond_it1.302
r_mcangle_it1.073
r_mcbond_it0.552
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.642
r_dihedral_angle_3_deg17.749
r_dihedral_angle_4_deg15.265
r_dihedral_angle_1_deg5.634
r_scangle_it2.275
r_angle_refined_deg1.437
r_scbond_it1.302
r_mcangle_it1.073
r_mcbond_it0.552
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9282
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms870

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing