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Crystal structure of Rat TOM20-ALDH presequence complex: The intermolecular disulfide bond was cleaved in the crystal of a disulfide-tethered complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V1T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.09M MES pH6.0, 0.045M MgCl2, 24% PEG 3350, 10mM DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.73 28.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.77 α = 90 b = 27.723 β = 102.71 c = 70.812 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4r 2007-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.00 SPring-8 BL38B1
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 2 69.01 98.3 0.089 11 3.4 8876 8725
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 2 2.07 89.1 0.296 2.4 786
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 2V1T 2 50 8221 405 96.78 0.20813 0.20609 0.2059 0.25073 0.2505 RANDOM 24.663
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] 1.95 -0.01 -0.84 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.597 r_dihedral_angle_3_deg 20.652 r_dihedral_angle_4_deg 14.067 r_dihedral_angle_1_deg 4.945 r_scangle_it 3.713 r_scbond_it 2.253 r_mcangle_it 1.535 r_angle_refined_deg 1.421 r_mcbond_it 0.779 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.597 r_dihedral_angle_3_deg 20.652 r_dihedral_angle_4_deg 14.067 r_dihedral_angle_1_deg 4.945 r_scangle_it 3.713 r_scbond_it 2.253 r_mcangle_it 1.535 r_angle_refined_deg 1.421 r_mcbond_it 0.779 r_chiral_restr 0.096 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1234 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing