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Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum (apo form)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.1M TRIS (PH 7.5), 10% ISOPROPANOL, 10% PEG6000, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.55 51.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.183 α = 90 b = 112.035 β = 94.74 c = 98.317 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 90 CCD ADSC QUANTUM 210 2005-06-29 M SINGLE WAVELENGTH 2 1 x-ray 90 CCD ADSC QUANTUM 210 2005-06-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9792, 0.97936, 0.91837 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.12 50 91.1 0.055 30 643080
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.12 1.16 77.6 0.369 2.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.12 35.05 643080 33894 91.6 0.176 0.175 0.189 0.1792 RANDOM 14.05
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 -0.01 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.271 r_dihedral_angle_4_deg 14.593 r_dihedral_angle_3_deg 11.133 r_dihedral_angle_1_deg 5.842 r_scangle_it 1.791 r_scbond_it 1.238 r_angle_refined_deg 1.168 r_mcangle_it 0.734 r_mcbond_it 0.442 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.271 r_dihedral_angle_4_deg 14.593 r_dihedral_angle_3_deg 11.133 r_dihedral_angle_1_deg 5.842 r_scangle_it 1.791 r_scbond_it 1.238 r_angle_refined_deg 1.168 r_mcangle_it 0.734 r_mcbond_it 0.442 r_nbtor_refined 0.301 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.13 r_chiral_restr 0.075 r_symmetry_hbond_refined 0.074 r_xyhbond_nbd_refined 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_refined 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 13475 Nucleic Acid Atoms Solvent Atoms 3383 Heterogen Atoms 82
Software Software Software Name Purpose SOLVE phasing REFMAC refinement HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling