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Crystal structure of atu4361 sugar transporter from Agrobacterium Fabrum C58, target efi-510558, with bound sucrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QSC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 2.09 CRYSTALLIZATION CONDITIONS, PROTEIN: 10 MM BIS-TRIS, 500 MM NACL, 5% GLYCEROL, 5 MM DTT, TEV PROTEASE (1:100 RATIO); RESERVOIR: 0.1M TRIS-HCL, PH 8.5, 30% PEG400; CRYOPROTECTION: RESERVOIR PLUS 200MM SUCROSE; VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.08 40.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.025 α = 90 b = 76.564 β = 90.21 c = 67.873 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 PIXEL PSI PILATUS 6M MIRRORS 2014-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
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 1.34 50 97.9 0.037 0.037 13.2 4.3 80477 -5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.34 1.36 52.2 0.46 0.46 2.8 3.6
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 MOLECULAR REPLACEMENT THROUGHOUT 4QSC 1.34 50 78001 2317 97.7 0.122 0.121 0.1383 0.151 0.1672 RANDOM 23.13
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] -0.48 0.05 0.04 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.958 r_sphericity_free 23.17 r_dihedral_angle_4_deg 18.461 r_dihedral_angle_3_deg 14.179 r_sphericity_bonded 10.732 r_rigid_bond_restr 6.122 r_dihedral_angle_1_deg 6.056 r_scbond_it 4.347 r_scbond_other 4.347 r_long_range_B_refined 4.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.958 r_sphericity_free 23.17 r_dihedral_angle_4_deg 18.461 r_dihedral_angle_3_deg 14.179 r_sphericity_bonded 10.732 r_rigid_bond_restr 6.122 r_dihedral_angle_1_deg 6.056 r_scbond_it 4.347 r_scbond_other 4.347 r_long_range_B_refined 4.142 r_long_range_B_other 4.142 r_scangle_other 3.99 r_mcangle_other 2.564 r_mcangle_it 2.553 r_mcbond_it 2.498 r_mcbond_other 2.484 r_angle_refined_deg 1.936 r_angle_other_deg 1.044 r_chiral_restr 0.195 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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 2965 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 69
Software Software Software Name Purpose SHELX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing