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Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complexes with products
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1M MES (pH6.0), 15% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 39.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.519 α = 90 b = 70.878 β = 90 c = 170.979 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 2005-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 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 1.8 171.5 96.8 0.159 12.1 71461 69085
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) 1.8 1.86 96.7 0.383 12.1 7005
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 1.8 35.63 67841 3618 96.64 0.18186 0.17984 0.1776 0.21886 0.2142 RANDOM 28.3
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] -0.53 0.69 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.436 r_dihedral_angle_4_deg 17.257 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_1_deg 6.519 r_scangle_it 3.226 r_scbond_it 2.182 r_angle_refined_deg 1.46 r_mcangle_it 1.328 r_mcbond_it 0.875 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.436 r_dihedral_angle_4_deg 17.257 r_dihedral_angle_3_deg 14.106 r_dihedral_angle_1_deg 6.519 r_scangle_it 3.226 r_scbond_it 2.182 r_angle_refined_deg 1.46 r_mcangle_it 1.328 r_mcbond_it 0.875 r_nbtor_refined 0.303 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.178 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.101 r_metal_ion_refined 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 6753 Nucleic Acid Atoms Solvent Atoms 552 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing