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Crystal Structure of SecYE translocon from Thermus thermophilus with a Fab fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 11% PEG 1500, 0.1M HEPES-Na (pH 7.5), 0.14M ammonium formate, 0.02% n-Dodecyl-beta-D-maltoside, 0.002M zinc acetate, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.59 65.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 189.096 α = 90 b = 103.073 β = 105.18 c = 78.005 γ = 90
Symmetry Space Group C 1 2 1
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 2007-10-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 210 2006-10-25 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.97942 SPring-8 BL41XU 2 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.97920,0.97942,0.96418 Photon Factory AR-NW12A
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 1,2 3.2 48.43 22585
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 3.2 48.43 22465 1212 98.62 0.24604 0.24424 0.2565 0.2798 0.2546 RANDOM 127.5
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] -4.64 3.82 1.58 5.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.62 r_dihedral_angle_4_deg 21.039 r_dihedral_angle_3_deg 19.415 r_dihedral_angle_1_deg 6.1 r_angle_refined_deg 1.148 r_scangle_it 0.899 r_mcangle_it 0.636 r_scbond_it 0.514 r_mcbond_it 0.353 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.62 r_dihedral_angle_4_deg 21.039 r_dihedral_angle_3_deg 19.415 r_dihedral_angle_1_deg 6.1 r_angle_refined_deg 1.148 r_scangle_it 0.899 r_mcangle_it 0.636 r_scbond_it 0.514 r_mcbond_it 0.353 r_nbtor_refined 0.309 r_nbd_refined 0.219 r_metal_ion_refined 0.173 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.082 r_symmetry_hbond_refined 0.019 r_bond_refined_d 0.008 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_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 6930 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling SHARP phasing REFMAC refinement