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Crystal Structure of SecYE translocon from Thermus thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZJS the SecYE structure produced by MD simulation using 2ZJS structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 28.5% PEG 3350, 0.18M Na-citrate, 0.015% octaethylene glycol monododecyl ether, 5% glycerol, 0.0001M Pefabloc, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.64 73.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.876 α = 90 b = 91.876 β = 90 c = 240.56 γ = 90
Symmetry Space Group P 43 2 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 2008-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 6 50 93.4 2743
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 the SecYE structure produced by MD simulation using 2ZJS structure 6 42.92 2616 123 93.8 0.40884 0.40704 0.4126 0.44504 0.409 RANDOM 368.097
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] 0.31 0.31 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_3_deg 20.689 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_1_deg 7.515 r_angle_refined_deg 1.42 r_symmetry_vdw_refined 0.494 r_scangle_it 0.425 r_nbtor_refined 0.323 r_nbd_refined 0.276 r_scbond_it 0.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.285 r_dihedral_angle_3_deg 20.689 r_dihedral_angle_4_deg 20.115 r_dihedral_angle_1_deg 7.515 r_angle_refined_deg 1.42 r_symmetry_vdw_refined 0.494 r_scangle_it 0.425 r_nbtor_refined 0.323 r_nbd_refined 0.276 r_scbond_it 0.255 r_mcangle_it 0.246 r_xyhbond_nbd_refined 0.234 r_symmetry_hbond_refined 0.191 r_mcbond_it 0.139 r_chiral_restr 0.088 r_bond_refined_d 0.011 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 3594 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing