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Crystal structure of Tim40/MIA40, a disulfide relay system in mitochondria, solved as MBP fusion protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ANF PDB ENTRY 1ANF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 100mM KOAc, 200 mM NH4OAc, 30 % PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.263 α = 90 b = 101.403 β = 90 c = 109.355 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS VII 2008-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 90 99.6 0.092 16.6 12.6 9692 22.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 100 0.309 22.2 11.6 943
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ANF 3 31.33 9184 464 99.71 0.20905 0.20536 0.1993 0.27816 0.2003 RANDOM 8.356
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] -0.81 0.19 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.537 r_dihedral_angle_3_deg 20.088 r_dihedral_angle_4_deg 16.701 r_dihedral_angle_1_deg 5.853 r_scangle_it 1.338 r_angle_refined_deg 1.241 r_scbond_it 0.773 r_mcangle_it 0.623 r_mcbond_it 0.342 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.537 r_dihedral_angle_3_deg 20.088 r_dihedral_angle_4_deg 16.701 r_dihedral_angle_1_deg 5.853 r_scangle_it 1.338 r_angle_refined_deg 1.241 r_scbond_it 0.773 r_mcangle_it 0.623 r_mcbond_it 0.342 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.292 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.083 r_symmetry_hbond_refined 0.036 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 3506 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing