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Crystal structure of sugar transporter RHE_PF00321 from Rhizobium etli, target EFI-510806, an open conformation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 10% GLYCEROL, 5 MM DTT; RESERVOIR: 0.1M SODIUM ACETATE, 0.1M TRIS:HCL, PH 8.5, 30% PEG 4000; CRYOPROTECTION: RESERVOIR, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.995 α = 90 b = 110.52 β = 90 c = 137.276 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315 MIRRORS 2014-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 50 99.9 0.079 0.079 40.1 12.1 141707 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 100 2.2 11.9
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 SAD THROUGHOUT NONE 1.8 50 71816 2304 99.88 0.18495 0.18312 0.1922 0.24254 0.2463 RANDOM 46.292
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] 0.13 -0.77 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.851 r_dihedral_angle_4_deg 17.314 r_dihedral_angle_3_deg 15.691 r_scbond_it 14.141 r_scbond_other 14.139 r_scangle_other 13.637 r_long_range_B_other 13.15 r_long_range_B_refined 13.148 r_mcbond_it 9.234 r_mcbond_other 9.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.851 r_dihedral_angle_4_deg 17.314 r_dihedral_angle_3_deg 15.691 r_scbond_it 14.141 r_scbond_other 14.139 r_scangle_other 13.637 r_long_range_B_other 13.15 r_long_range_B_refined 13.148 r_mcbond_it 9.234 r_mcbond_other 9.219 r_mcangle_other 9.124 r_mcangle_it 9.122 r_dihedral_angle_1_deg 5.721 r_angle_refined_deg 1.48 r_angle_other_deg 0.824 r_chiral_restr 0.089 r_bond_refined_d 0.012 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 6088 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 6
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing