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The plug domain of the SecY protein stablizes the closed state of the translocation channel and maintains a membrane seal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RHZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 277 40-55% PEG400, 50mM Glycine-HCl, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.89 74.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.51 α = 90 b = 150.36 β = 90 c = 79.85 γ = 90
Symmetry Space Group P 21 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 200 CCD ADSC QUANTUM 315 2006-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97921 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.5 50 99.6 0.087 0.087 16.8 8 14808 14742 1.8 3.3 110
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.63 100 0.739 0.739 3.3 8 1449
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1RHZ 3.6 44.07 3.3 1.8 8359 465 65.71 0.29972 0.29782 0.2998 0.33457 0.3252 RANDOM 105.182
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] 4.96 -5.49 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.155 r_dihedral_angle_3_deg 20.64 r_dihedral_angle_4_deg 17.463 r_dihedral_angle_1_deg 5.443 r_angle_refined_deg 1.181 r_mcangle_it 0.918 r_scangle_it 0.729 r_mcbond_it 0.512 r_scbond_it 0.433 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.155 r_dihedral_angle_3_deg 20.64 r_dihedral_angle_4_deg 17.463 r_dihedral_angle_1_deg 5.443 r_angle_refined_deg 1.181 r_mcangle_it 0.918 r_scangle_it 0.729 r_mcbond_it 0.512 r_scbond_it 0.433 r_nbtor_refined 0.319 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.231 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3999 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling RESOLVE phasing