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Crystal structure of Toc33 from Arabidopsis thaliana in complex with Mg2+ and GMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H65 PDB ENTRY 1H65
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 296 22% PEG1500, 15% glycerol, pH7.4, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.71 54.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.567 α = 90 b = 121.567 β = 90 c = 42.879 γ = 90
Symmetry Space Group P 41 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 315 2006-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9746 ESRF ID23-1
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 2.84 25 99.6 0.085 15.39 5.8 7834 7827 -4 -3 69.8
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 2.84 2.94 100 0.486 2.2 6 748
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 1H65 2.85 25 7461 366 98.53 0.22082 0.21802 0.194 0.27663 0.2492 RANDOM 69.779
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] -0.29 -0.29 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.202 r_dihedral_angle_4_deg 26.122 r_dihedral_angle_3_deg 21.698 r_dihedral_angle_1_deg 9.626 r_scangle_it 2.961 r_angle_refined_deg 2.073 r_scbond_it 1.916 r_angle_other_deg 1.359 r_mcangle_it 1.325 r_mcbond_it 1.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.202 r_dihedral_angle_4_deg 26.122 r_dihedral_angle_3_deg 21.698 r_dihedral_angle_1_deg 9.626 r_scangle_it 2.961 r_angle_refined_deg 2.073 r_scbond_it 1.916 r_angle_other_deg 1.359 r_mcangle_it 1.325 r_mcbond_it 1.144 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.241 r_nbd_other 0.219 r_symmetry_vdw_other 0.193 r_symmetry_hbond_refined 0.189 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.103 r_mcbond_other 0.089 r_nbtor_other 0.086 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1885 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DNA data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing