3DEF

Crystal structure of Toc33 from Arabidopsis thaliana, dimerization deficient mutant R130A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.429220% PEG 3350, 0.2M NH4Cl, 20% Glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.4650.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.44α = 90
b = 71.44β = 90
c = 112.46γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Toroidal Zerodur mirror2007-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.963097.30.03737.26.92198421395-325
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.961.9996.50.2844.44.41052

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 3BB31.9627.7820125108295.350.173110.170970.21346RANDOM22.652
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]
-0.09-0.090.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.517
r_dihedral_angle_4_deg19.12
r_dihedral_angle_3_deg16.098
r_dihedral_angle_1_deg5.992
r_scangle_it4.519
r_scbond_it3.047
r_mcangle_it1.922
r_angle_refined_deg1.757
r_mcbond_it1.452
r_angle_other_deg1.024
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.517
r_dihedral_angle_4_deg19.12
r_dihedral_angle_3_deg16.098
r_dihedral_angle_1_deg5.992
r_scangle_it4.519
r_scbond_it3.047
r_mcangle_it1.922
r_angle_refined_deg1.757
r_mcbond_it1.452
r_angle_other_deg1.024
r_symmetry_vdw_refined0.404
r_symmetry_vdw_other0.325
r_mcbond_other0.299
r_nbd_refined0.222
r_nbd_other0.201
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.175
r_symmetry_hbond_refined0.138
r_chiral_restr0.12
r_nbtor_other0.089
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1901
Nucleic Acid Atoms
Solvent Atoms206
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing