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Crystal structure of carbohydrate transporter solute binding protein VEIS_2079 from Verminephrobacter eiseniae EF01-2, TARGET EFI-511009, a complex with D-TALITOL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-TALITOL) RESERVOIR: 0.2 M POTASSIUM SULFATE, 25% PEG3350 CRYOPROTECTION: RESERVOIR SOLUTION PLUS 25% (V/V) GLYCEROL VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.22 44.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.65 α = 90 b = 68.635 β = 90 c = 120.376 γ = 90
Symmetry Space Group P 2 2 21
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 97.5 0.095 33.9 15 113208 -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 95.4 0.98 2.8 13.9
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 25 106509 3259 97.58 0.12403 0.12322 0.1369 0.1509 0.1572 RANDOM 18.091
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] 0.39 0.48 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.603 r_sphericity_free 24.359 r_dihedral_angle_3_deg 12.469 r_sphericity_bonded 11.595 r_dihedral_angle_4_deg 11.41 r_scbond_other 7.199 r_scbond_it 7.193 r_scangle_other 6.016 r_dihedral_angle_1_deg 5.789 r_long_range_B_refined 4.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.603 r_sphericity_free 24.359 r_dihedral_angle_3_deg 12.469 r_sphericity_bonded 11.595 r_dihedral_angle_4_deg 11.41 r_scbond_other 7.199 r_scbond_it 7.193 r_scangle_other 6.016 r_dihedral_angle_1_deg 5.789 r_long_range_B_refined 4.754 r_long_range_B_other 4.753 r_rigid_bond_restr 2.957 r_mcangle_it 2.155 r_mcangle_other 2.154 r_mcbond_it 2.087 r_mcbond_other 2.087 r_angle_refined_deg 1.687 r_angle_other_deg 0.949 r_chiral_restr 0.242 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 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 4394 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 112
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing