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Crystal structure of 5-methylthioribose transporter solute binding protein TLET_1677 from Thermotoga lettingae TMO TARGET EFI-511109 in complex with 5-methylthioribose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT); RESERVOIR: 0.1 M HEPES-NAOH, PH 7.5, 0.2 M MAGNESIUM CHLORIDE, 30% PPG P400; CRYOPROTECTION: RESERVOIR SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K;
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.622 α = 91.83 b = 67.848 β = 92.39 c = 83.653 γ = 89.93
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 RAYONIX MX225HE MIRRORS 2014-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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 1.75 50 97.1 0.137 10 3.9 128230 -3
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 1.75 1.78 94.9 0.71 2.1 3.6
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 SAD THROUGHOUT 1.75 50 119981 3771 96.95 0.21593 0.21444 0.2235 0.26356 0.2704 RANDOM 33.26
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] -3.67 -0.31 -0.41 -3.8 0.37 7.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.484 r_dihedral_angle_4_deg 20.369 r_dihedral_angle_3_deg 14.933 r_long_range_B_refined 11.642 r_long_range_B_other 11.642 r_scangle_other 11.181 r_scbond_it 10.856 r_scbond_other 10.855 r_dihedral_angle_1_deg 6.368 r_mcangle_other 6.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.484 r_dihedral_angle_4_deg 20.369 r_dihedral_angle_3_deg 14.933 r_long_range_B_refined 11.642 r_long_range_B_other 11.642 r_scangle_other 11.181 r_scbond_it 10.856 r_scbond_other 10.855 r_dihedral_angle_1_deg 6.368 r_mcangle_other 6.184 r_mcangle_it 6.182 r_mcbond_it 5.672 r_mcbond_other 5.665 r_angle_refined_deg 1.601 r_angle_other_deg 0.835 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9868 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms 44
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing