4KT0

Crystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC 6803


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JB0PDB entry 1JB0 with truncated side chains and chlorophyll tails

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52784.5% PEG3350, 30mM Tricine-NaOH pH8, 55mM NaCl, 50mM Glycine, 0.005% Nonyl- beta -D-Maltoside., pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
3.9468.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.179α = 90
b = 173.308β = 90
c = 179.136γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

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
12.83099.40.1397.94.692450918951161.4
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)
12.82.952.3821.14.1

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 1JB0 with truncated side chains and chlorophyll tails2.829.9771.359251891218455898.610.20.19770.244694.61
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d28.249
f_angle_d1.734
f_chiral_restr0.046
f_plane_restr0.012
f_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15758
Nucleic Acid Atoms
Solvent Atoms29
Heterogen Atoms6264

Software

Software
Software NamePurpose
XDSdata scaling
MOLREPphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling