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Crystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TF2 PDB ENTRY 1TF2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 298 20% PEG 3350, 200mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.32 71.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.616 α = 90 b = 156.003 β = 90 c = 358.155 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 100 CCD ADSC QUANTUM 315 Cryogenically cooled first crystal, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2007-08-15 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry 2007-10-17 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD ADSC QUANTUM 315 sagitally bent second mono crystal with 4:1 magnification ratio and vertically focusing mirror 2008-02-29 M SINGLE WAVELENGTH 1,2,3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97950 APS 19-ID 2 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97950 APS 24-ID-C 3 SYNCHROTRON NSLS BEAMLINE X29A 0.97950 NSLS X29A
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 1,2,3 4.5 50 97.7 0.065 16.1 11.6 34733
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) 1,2,3 4.5 4.77 89.7 0.85 2 8.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 SAD, MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1TF2 4.5 15 2 34733 34733 3269 97.7 0.279 0.279 0.2861 0.303 0.2895 RANDOM 358.2
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] 9.68 13.17 -22.85
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_angle_deg 1.3 c_improper_angle_d 0.87 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21 c_angle_deg 1.3 c_improper_angle_d 0.87 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21304 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 64
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing SOLVE phasing DM phasing CNS refinement PDB_EXTRACT data extraction