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Bifidobacterium asteroides alpha-L-fucosidase (TT1819) in complex with fucose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ODU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.12M Diethylene glycol; 0.12M Triethylene
glycol; 0.12M Tetraethylene glycol; 0.12M
Pentaethylene glycol, 0.1M Tris (base); BICINE pH 8.5, 10% v/v MPD; 10% PEG
1000; 10% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.32 46.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.058 α = 90 b = 142.765 β = 90 c = 167.202 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 PIXEL DECTRIS PILATUS3 X 6M 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97625 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 108.56 100 0.246 0.262 0.086 0.998 9.2 17.5 167861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 9.946 10.726 3.866 0.215 14.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 83.741 167720 8366 99.95 0.171 0.1689 0.1786 0.2069 0.2113 38.507
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] -1.975 1.839 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.697 r_dihedral_angle_3_deg 15.236 r_dihedral_angle_2_deg 14.914 r_lrange_it 7.313 r_lrange_other 7.309 r_dihedral_angle_1_deg 6.668 r_scangle_it 6.302 r_scangle_other 6.302 r_scbond_it 4.595 r_scbond_other 4.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.697 r_dihedral_angle_3_deg 15.236 r_dihedral_angle_2_deg 14.914 r_lrange_it 7.313 r_lrange_other 7.309 r_dihedral_angle_1_deg 6.668 r_scangle_it 6.302 r_scangle_other 6.302 r_scbond_it 4.595 r_scbond_other 4.595 r_mcangle_it 4.192 r_mcangle_other 4.192 r_mcbond_it 3.282 r_mcbond_other 3.273 r_angle_refined_deg 1.924 r_angle_other_deg 0.646 r_nbd_other 0.308 r_symmetry_nbd_refined 0.238 r_nbd_refined 0.229 r_symmetry_xyhbond_nbd_refined 0.228 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_5 0.074 r_ncsr_local_group_9 0.07 r_ncsr_local_group_3 0.067 r_ncsr_local_group_4 0.067 r_ncsr_local_group_1 0.066 r_ncsr_local_group_7 0.066 r_ncsr_local_group_6 0.065 r_ncsr_local_group_2 0.063 r_symmetry_xyhbond_nbd_other 0.061 r_ncsr_local_group_8 0.06 r_ncsr_local_group_10 0.06 r_ncsr_local_group_12 0.058 r_ncsr_local_group_15 0.058 r_ncsr_local_group_14 0.057 r_ncsr_local_group_13 0.055 r_ncsr_local_group_11 0.053 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16170 Nucleic Acid Atoms Solvent Atoms 733 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing