3V3Z

I(L177)H mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E6D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42893.5% 1,2,3 -heptanetriol, 2% dioxane, 0.1% LDAO, 1M potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
5.7778.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.13α = 90
b = 140.13β = 90
c = 186.03γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2011-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8123EMBL/DESY, HAMBURGX13

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
12.928.996.50.09214.254.614738445707
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)
12.9390.20.6642.34.55

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 REPLACEMENTTHROUGHOUT1E6D2.928.9457074342122861000.2120.206260.203940.25063RANDOM69.052
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]
1.390.691.39-2.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.879
r_dihedral_angle_4_deg18.743
r_dihedral_angle_3_deg17.35
r_dihedral_angle_1_deg5.639
r_scangle_it1.862
r_angle_refined_deg1.72
r_scbond_it1.056
r_mcangle_it0.896
r_mcbond_it0.468
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.879
r_dihedral_angle_4_deg18.743
r_dihedral_angle_3_deg17.35
r_dihedral_angle_1_deg5.639
r_scangle_it1.862
r_angle_refined_deg1.72
r_scbond_it1.056
r_mcangle_it0.896
r_mcbond_it0.468
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6484
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms683

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction