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Crystal structure of ribose transporter solute binding protein RHE_PF00037 from Rhizobium etli CFN 42, TARGET EFI-511357, in complex with D-ribose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-RIBOSE); RESERVOIR: 0.2 M CALCIUM CHLORIDE, 0.1 M TRIS-HCL, PH 8.5, 20% (w/v) PEG 4000; CRYOPROTECTION: RESERVOIR SOLUTION PLUS 20% D-GLUCOSE SOLUTION; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.11 α = 90 b = 36.766 β = 117.91 c = 95.48 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 RAYONIX MX225HE MIRRORS 2014-12-05 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 1.4 50 98 0.103 22.2 7.5 57304 -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 1.4 1.42 96.6 0.8 2.57 7.5
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 1.4 24 53653 1724 97.66 0.1446 0.14341 0.1576 0.18106 0.1954 RANDOM 19.268
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] -0.65 -1.08 3.84 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.674 r_sphericity_free 30.549 r_sphericity_bonded 15.754 r_dihedral_angle_3_deg 14.736 r_dihedral_angle_4_deg 10.484 r_scbond_it 7.959 r_scbond_other 7.959 r_scangle_other 6.98 r_long_range_B_refined 6.434 r_long_range_B_other 6.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.674 r_sphericity_free 30.549 r_sphericity_bonded 15.754 r_dihedral_angle_3_deg 14.736 r_dihedral_angle_4_deg 10.484 r_scbond_it 7.959 r_scbond_other 7.959 r_scangle_other 6.98 r_long_range_B_refined 6.434 r_long_range_B_other 6.34 r_dihedral_angle_1_deg 5.661 r_rigid_bond_restr 4.404 r_mcangle_other 3.337 r_mcangle_it 3.314 r_mcbond_other 3.232 r_mcbond_it 3.196 r_angle_refined_deg 1.537 r_angle_other_deg 1.448 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2120 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 12
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing