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Bifidobacterium asteroides alpha-L-fucosidase (TT1819) catalytic mutant.
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 0.1 M Sodium acetate pH 4.6, 8% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.1 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.684 α = 90 b = 136.252 β = 90 c = 160.451 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 S 6M 2018-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96862 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.659 104.074 99.1 0.204 0.044 0.997 11.1 21.1 224526
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.69 0.804 0.304 0.503 1.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.659 104.074 224428 11112 99.05 0.161 0.1601 0.1722 0.1875 0.1968 random selection 15.675
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] -0.438 -0.099 0.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.52 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_2_deg 10.157 r_dihedral_angle_1_deg 6.524 r_lrange_it 5.546 r_lrange_other 5.456 r_scangle_it 3.364 r_scangle_other 3.363 r_mcangle_it 2.505 r_mcangle_other 2.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.52 r_dihedral_angle_3_deg 14.665 r_dihedral_angle_2_deg 10.157 r_dihedral_angle_1_deg 6.524 r_lrange_it 5.546 r_lrange_other 5.456 r_scangle_it 3.364 r_scangle_other 3.363 r_mcangle_it 2.505 r_mcangle_other 2.505 r_scbond_it 2.112 r_scbond_other 2.112 r_angle_refined_deg 1.608 r_mcbond_it 1.526 r_mcbond_other 1.526 r_angle_other_deg 0.568 r_symmetry_nbd_refined 0.279 r_nbd_other 0.245 r_nbd_refined 0.229 r_symmetry_xyhbond_nbd_refined 0.226 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.175 r_ncsr_local_group_12 0.108 r_ncsr_local_group_2 0.1 r_ncsr_local_group_5 0.093 r_ncsr_local_group_6 0.093 r_ncsr_local_group_11 0.09 r_ncsr_local_group_10 0.089 r_chiral_restr 0.086 r_ncsr_local_group_15 0.086 r_ncsr_local_group_9 0.085 r_ncsr_local_group_14 0.085 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_4 0.077 r_ncsr_local_group_3 0.076 r_ncsr_local_group_8 0.075 r_symmetry_xyhbond_nbd_other 0.069 r_ncsr_local_group_1 0.066 r_ncsr_local_group_13 0.066 r_ncsr_local_group_7 0.065 r_bond_refined_d 0.012 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 16105 Nucleic Acid Atoms Solvent Atoms 1883 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling MOLREP phasing