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Structure and activity of the GH20 beta-N-beta-N-acetylhexosaminidase from Bifidobacterium bifidum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other generated by MrBUMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 21.6 mg/mL of purified protein in the buffer of tris 25 mM pH 8.0 and NaCl 200 mM is mixed with PEG 3350 23%, 0.1 M bis-tris propane PH 6.5 and 0.2 M NaBr at 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.566 α = 90 b = 126.75 β = 90 c = 152.71 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 EIGER2 XE 16M 2019-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.75 63.38 100 0.997 9 7.4 111519
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 1.75 1.78 100 1.654 0.969 0.61 1.1 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 generated by MrBUMP 1.75 63.38 111416 5615 99.947 0.163 0.1601 0.1703 0.2197 0.2246 27.359
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] -3.781 1.429 2.352
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.127 r_dihedral_angle_4_deg 15.553 r_dihedral_angle_3_deg 12.33 r_dihedral_angle_1_deg 7.043 r_lrange_it 6.574 r_lrange_other 6.329 r_scangle_it 5.819 r_scangle_other 5.818 r_mcangle_it 5.197 r_mcangle_other 5.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.127 r_dihedral_angle_4_deg 15.553 r_dihedral_angle_3_deg 12.33 r_dihedral_angle_1_deg 7.043 r_lrange_it 6.574 r_lrange_other 6.329 r_scangle_it 5.819 r_scangle_other 5.818 r_mcangle_it 5.197 r_mcangle_other 5.197 r_scbond_other 4.798 r_scbond_it 4.797 r_mcbond_it 4.325 r_mcbond_other 4.323 r_rigid_bond_restr 3.102 r_angle_refined_deg 1.511 r_angle_other_deg 1.41 r_nbd_other 0.212 r_nbd_refined 0.204 r_symmetry_nbd_refined 0.2 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.159 r_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.072 r_metal_ion_refined 0.023 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5290 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling SHELXDE phasing