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Crystal structure of the glucose-binding protein SAR11_0769 from "Candidatus Pelagibacter ubique" HTCC1062 bound to glucose
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, HANGING DROP 6.5 293 1 uL 12 mg/mL protein + 1 uL 18.5% (w/v) PEG 1500, 10% (v/v) isopropanol, 0.1 M Bis-Tris pH 6.5. Crystal was cryoprotected in 15% (w/v) PEG 1500, 30% (v/v) ethylene glycol, 10% (v/v) isopropanol, 0.1 M Bis-Tris pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.11 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.642 α = 90 b = 44.642 β = 90 c = 329.112 γ = 120
Symmetry Space Group P 32 2 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 DECTRIS EIGER X 9M 2022-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.00000 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.86 47.02 99 0.239 0.248 0.986 6.28 12 33089
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.98 94.4 0.521 0.545 0.913 1.08 9.49
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold 1.86 38.4 1.35 33030 1608 98.79 0.2054 0.2037 0.2369 0.2504
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.348 f_angle_d 0.931 f_chiral_restr 0.054 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2960 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing