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Blood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium bifidum, construct T7-tag_24-673
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Model to be deposited
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 15% (w/v) PEG 20000, 0.1M MES-NaOH pH 6.5 (Seed condition: 10% (w/v) PEG 6000, 0.1M citric acid pH 5.0, 4 degrees celsius)
Crystal Properties Matthews coefficient Solvent content 2.95 58.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.34 α = 90 b = 73.154 β = 91.38 c = 177.968 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 80 PIXEL DECTRIS EIGER X 4M 2020-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.0800 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.5 47.88 99.9 0.76 2.9 3.4 20905 19.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.83 0.35
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.5 47.88 1.95 20884 1111 99.92 0.2072 0.2028 0.2029 0.2848 0.285 RANDOM 17.8
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 14.8891 f_angle_d 1.0484 f_chiral_restr 0.0577 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9432 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing