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Crystal structure of Acidovorax avenae L-fucose mutarotase (L-fucose-bound form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.8 M potassium sodium tartrate, 0.1 M Tris-HCl pH 8.5, 0.5% PEGMME 5000
Crystal Properties Matthews coefficient Solvent content 3.3 62.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.398 α = 90 b = 68.398 β = 90 c = 69.102 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 2020-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.75 50 99.9 0.062 0.065 0.02 0.999 17.4 10.3 36466
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 97.8 1.216 1.285 0.411 0.634 1.9 9.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7BYU 1.75 44.9876 1.97 36430 1825 99.86 0.2273 0.2262 0.2306 0.2466 0.2498 41.1657
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1798 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 56
Software Software Software Name Purpose XDS data processing PHENIX refinement PDB_EXTRACT data extraction Coot model building PHASER phasing Aimless data scaling