2ZXT

Crystal structure of Tim40/MIA40, a disulfide relay system in mitochondria, solved as MBP fusion protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293100mM KOAc, 200 mM NH4OAc, 30 % PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.263α = 90
b = 101.403β = 90
c = 109.355γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS VII2008-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54

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
139099.60.09216.612.6969222.6
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)
133.111000.30922.211.6943

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 1ANF331.33918446499.710.209050.205360.27816RANDOM8.356
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]
-0.810.190.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.537
r_dihedral_angle_3_deg20.088
r_dihedral_angle_4_deg16.701
r_dihedral_angle_1_deg5.853
r_scangle_it1.338
r_angle_refined_deg1.241
r_scbond_it0.773
r_mcangle_it0.623
r_mcbond_it0.342
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.537
r_dihedral_angle_3_deg20.088
r_dihedral_angle_4_deg16.701
r_dihedral_angle_1_deg5.853
r_scangle_it1.338
r_angle_refined_deg1.241
r_scbond_it0.773
r_mcangle_it0.623
r_mcbond_it0.342
r_nbtor_refined0.31
r_symmetry_vdw_refined0.292
r_nbd_refined0.213
r_xyhbond_nbd_refined0.145
r_chiral_restr0.083
r_symmetry_hbond_refined0.036
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3506
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing