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Crystal structure of alpha-1,3/4-fucosidase from Bifidobacterium longum subsp. infantis D172A/E217A mutant complexed with lacto-N-fucopentaose II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MO4 PDB ENTRY 3MO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1M sodium citrate buffer (pH 5.5), 20% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.588 α = 90 b = 105.971 β = 90 c = 120.715 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2011-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 96.4 0.104 16.6 5.9 62699 60403 25.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 95.4 0.474 2.6 5.2 2966
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3MO4 2.1 32.05 60403 57111 3047 96.02 0.17509 0.17509 0.17254 0.22295 0.2001 RANDOM 29.84
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.22 r_dihedral_angle_4_deg 20.116 r_dihedral_angle_3_deg 15.836 r_dihedral_angle_1_deg 6.509 r_angle_refined_deg 1.987 r_chiral_restr 0.133 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.22 r_dihedral_angle_4_deg 20.116 r_dihedral_angle_3_deg 15.836 r_dihedral_angle_1_deg 6.509 r_angle_refined_deg 1.987 r_chiral_restr 0.133 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7138 Nucleic Acid Atoms Solvent Atoms 463 Heterogen Atoms 82
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling