4HEA

Crystal structure of the entire respiratory complex I from Thermus thermophilus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I9VPDB entries 3I9V and 4HE8
experimental modelPDB 4HE8PDB entries 3I9V and 4HE8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6295100 mM Bis-Tris pH 6.0, 19% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 2.2 mM FOS-CHOLINE-8 fluorinated , VAPOR DIFFUSION, SITTING DROP, temperature 295K
2VAPOR DIFFUSION, SITTING DROP6295100 mM Bis-Tris pH 6.0, 24% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 50 mM NDSB-201, VAPOR DIFFUSION, SITTING DROP, temperature 295K
3VAPOR DIFFUSION, SITTING DROP6295100 mM Bis-Tris pH 6.0, 26% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.6% DDM, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.28α = 90
b = 340.89β = 100.57
c = 263.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6Mmirrors2011-09-23MSINGLE WAVELENGTH
22x-ray100PIXELPSI PILATUS 6Mmirrors2011-12-03MSINGLE WAVELENGTH
33x-ray100PIXELPSI PILATUS 6Mmirrors2011-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9ESRFID29
2SYNCHROTRONESRF BEAMLINE ID290.9ESRFID29
3SYNCHROTRONESRF BEAMLINE ID290.9ESRFID29

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
1,2,33.34099.50.2510.2515.16.124792024792099
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)
1,2,33.33.48991.8691.86915.6

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entries 3I9V and 4HE83.302739.998233383233383242793.660.20340.20240.2393Random, using lattice symmetry information (PHENIX).74.4
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_d18.03
f_angle_d1.467
f_chiral_restr0.111
f_bond_d0.008
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms73808
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms190

Software

Software
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling