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Crystal structure of the NTE domain of SusCdex (BT3090) dextran transporter
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.2 43.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.084 α = 90 b = 62.084 β = 90 c = 53.202 γ = 120
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 DECTRIS PILATUS 6M 2022-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.89844 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 23.99 99.7 0.046 0.051 0.022 1 21.4 9.8 15041
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.42 96.7 0.632 0.782 0.451 0.712 1.8 5.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.4 23.99 15038 773 99.735 0.176 0.1749 0.1758 0.2064 0.2067 22.406
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] 0.218 0.109 0.218 -0.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.478 r_dihedral_angle_3_deg 10.747 r_lrange_it 8.88 r_dihedral_angle_1_deg 6.845 r_scangle_it 4.928 r_scbond_it 3.602 r_mcangle_it 2.337 r_angle_refined_deg 2.195 r_mcbond_it 1.71 r_symmetry_nbd_refined 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.478 r_dihedral_angle_3_deg 10.747 r_lrange_it 8.88 r_dihedral_angle_1_deg 6.845 r_scangle_it 4.928 r_scbond_it 3.602 r_mcangle_it 2.337 r_angle_refined_deg 2.195 r_mcbond_it 1.71 r_symmetry_nbd_refined 0.362 r_nbtor_refined 0.298 r_xyhbond_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.215 r_nbd_refined 0.21 r_chiral_restr 0.108 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 590 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data collection PHASER phasing Coot model building