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Structure of Bifidobacterium bifidum GH20 beta-N-beta-N-acetylhexosaminidase E553Q variant in complex with 4MU-6SGlcNAc-derived oxazoline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YXZ
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 21%, 0.1 M BIS-TRIS PROPANE PH 6.5 AND 0.2 M NANO3 AT 1:1
Crystal Properties Matthews coefficient Solvent content 2.38 48.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.423 α = 90 b = 124.884 β = 90 c = 151.682 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 EIGER X 16M 2020-03-02 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) R Merge I (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 1.67 64.82 100 0.116 0.996 7.4 7 120710
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 0.732 0.755 1 6.9
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 6YXZ 1.67 64.82 120604 6030 99.938 0.163 0.1604 0.1712 0.2055 0.2134 26.849
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] 1.842 -0.959 -0.883
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.727 r_dihedral_angle_4_deg 16.402 r_dihedral_angle_3_deg 13.251 r_dihedral_angle_1_deg 7.166 r_lrange_it 4.983 r_lrange_other 4.734 r_scangle_it 4.531 r_scangle_other 4.53 r_mcangle_it 3.675 r_mcangle_other 3.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.727 r_dihedral_angle_4_deg 16.402 r_dihedral_angle_3_deg 13.251 r_dihedral_angle_1_deg 7.166 r_lrange_it 4.983 r_lrange_other 4.734 r_scangle_it 4.531 r_scangle_other 4.53 r_mcangle_it 3.675 r_mcangle_other 3.675 r_scbond_it 3.643 r_scbond_other 3.643 r_mcbond_it 2.956 r_mcbond_other 2.954 r_rigid_bond_restr 2.059 r_angle_refined_deg 1.44 r_angle_other_deg 1.39 r_nbd_other 0.226 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.202 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.142 r_metal_ion_refined 0.111 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.068 r_chiral_restr_other 0.065 r_symmetry_xyhbond_nbd_other 0.056 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5264 Nucleic Acid Atoms Solvent Atoms 653 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing