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Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complex with deoxyfuconojirimycin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 0.1M Tris (pH7.0), 10% iso-propanol, 10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.56 51.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.668 α = 90 b = 111.702 β = 95.31 c = 98.346 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 100 CCD ADSC QUANTUM 315 2005-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 98.06 100 0.112 7.2 113829 113799
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) 2.1 2.18 99.8 0.337 6.6 11323
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 (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 THROUGHOUT 2.1 48.97 108104 5697 99.92 0.15264 0.15024 0.1508 0.19757 0.1958 RANDOM 17.022
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] 0.16 -1.12 -0.98 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.552 r_dihedral_angle_4_deg 20.015 r_dihedral_angle_3_deg 13.624 r_dihedral_angle_1_deg 6.326 r_scangle_it 3.392 r_scbond_it 2.296 r_angle_refined_deg 1.505 r_mcangle_it 1.31 r_mcbond_it 0.827 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.552 r_dihedral_angle_4_deg 20.015 r_dihedral_angle_3_deg 13.624 r_dihedral_angle_1_deg 6.326 r_scangle_it 3.392 r_scbond_it 2.296 r_angle_refined_deg 1.505 r_mcangle_it 1.31 r_mcbond_it 0.827 r_nbtor_refined 0.303 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.174 r_symmetry_vdw_refined 0.164 r_xyhbond_nbd_refined 0.155 r_metal_ion_refined 0.102 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13462 Nucleic Acid Atoms Solvent Atoms 1685 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing