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Crystal structure of Toc33 from Arabidopsis thaliana in complex with GDP and Mg2+
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, HANGING DROP 7.4 292 24% PEG1500, 20% Glycerol, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.71 54.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.617 α = 90 b = 121.617 β = 90 c = 42.769 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 2006-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 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 2.9 29 99.3 0.081 14.4 6.1 7288 7234 -4 -3 82
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 2.94 3.04 97.9 0.466 1.9 4.2 702
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 2.94 25 6866 335 99.52 0.22006 0.218 0.187 0.26196 0.2328 RANDOM 104.928
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] -2.14 -2.14 4.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.329 r_dihedral_angle_3_deg 21.593 r_dihedral_angle_4_deg 17.793 r_dihedral_angle_1_deg 7.561 r_scangle_it 3.118 r_angle_refined_deg 2.057 r_scbond_it 1.99 r_mcangle_it 1.379 r_mcbond_it 0.85 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.329 r_dihedral_angle_3_deg 21.593 r_dihedral_angle_4_deg 17.793 r_dihedral_angle_1_deg 7.561 r_scangle_it 3.118 r_angle_refined_deg 2.057 r_scbond_it 1.99 r_mcangle_it 1.379 r_mcbond_it 0.85 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.249 r_symmetry_hbond_refined 0.245 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1894 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DNA data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing