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Crystal structure of Toc33 from Arabidopsis thaliana, dimerization deficient mutant R130A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BB3 PDB entry 3BB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 292 20% PEG 3350, 0.2M NH4Cl, 20% Glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.46 50.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.44 α = 90 b = 71.44 β = 90 c = 112.46 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 Toroidal Zerodur mirror 2007-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.96 30 97.3 0.037 37.2 6.9 21984 21395 -3 25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 1.99 96.5 0.284 4.4 4.4 1052
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 3BB3 1.96 27.78 20125 1082 95.35 0.17311 0.17097 0.1779 0.21346 0.2188 RANDOM 22.652
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 -0.09 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.517 r_dihedral_angle_4_deg 19.12 r_dihedral_angle_3_deg 16.098 r_dihedral_angle_1_deg 5.992 r_scangle_it 4.519 r_scbond_it 3.047 r_mcangle_it 1.922 r_angle_refined_deg 1.757 r_mcbond_it 1.452 r_angle_other_deg 1.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.517 r_dihedral_angle_4_deg 19.12 r_dihedral_angle_3_deg 16.098 r_dihedral_angle_1_deg 5.992 r_scangle_it 4.519 r_scbond_it 3.047 r_mcangle_it 1.922 r_angle_refined_deg 1.757 r_mcbond_it 1.452 r_angle_other_deg 1.024 r_symmetry_vdw_refined 0.404 r_symmetry_vdw_other 0.325 r_mcbond_other 0.299 r_nbd_refined 0.222 r_nbd_other 0.201 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.138 r_chiral_restr 0.12 r_nbtor_other 0.089 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1901 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DNA data collection HKL-2000 data reduction SCALA data scaling MOLREP phasing