☰ Navigation Tabs
Crystal structure of abc transporter solute binding protein AVI_3567 from AGROBACTERIUM VITIS S4, TARGET EFI-510645, with bound D-mannitol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 PROTEIN (10 MM HEPES PH 7.5, 5 MM DTT, 10 MM D-MANNITOL), RESERVOIR: 0.085 M TRIS-HCL, PH 8.5, 0.17 M SODIUM ACETATE, 25% PEG3350, 15% (V/V) GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.48 50.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.413 α = 90 b = 61.256 β = 104.01 c = 65.501 γ = 90
Symmetry Space Group P 1 21 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 1.5 50 99.3 0.122 12.95 7.5 73250 -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 1.5 1.53 98.4 0.49 4.5 7.4
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 1.5 25 69767 2178 98.37 0.13314 0.13204 0.148 0.16824 0.1838 RANDOM 24.318
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] 0.77 -0.99 -0.79 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.747 r_sphericity_free 23.465 r_dihedral_angle_4_deg 19.609 r_sphericity_bonded 14.332 r_dihedral_angle_3_deg 13.48 r_scbond_it 7.253 r_scbond_other 7.252 r_scangle_other 6.365 r_dihedral_angle_1_deg 5.834 r_long_range_B_refined 5.705
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.747 r_sphericity_free 23.465 r_dihedral_angle_4_deg 19.609 r_sphericity_bonded 14.332 r_dihedral_angle_3_deg 13.48 r_scbond_it 7.253 r_scbond_other 7.252 r_scangle_other 6.365 r_dihedral_angle_1_deg 5.834 r_long_range_B_refined 5.705 r_long_range_B_other 5.705 r_mcangle_other 3.855 r_mcangle_it 3.854 r_mcbond_it 3.367 r_mcbond_other 3.365 r_rigid_bond_restr 3.294 r_angle_refined_deg 1.565 r_angle_other_deg 0.91 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3234 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 16
Software Software Software Name Purpose SHELX model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing