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Glycosidase Wild Type at pH4.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2 M Ammonium citrate (pH 7.0), 8% PEG monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.84 56.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.345 α = 90 b = 105.345 β = 90 c = 90.328 γ = 90
Symmetry Space Group P 4 21 2
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 2M 2019-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.8 47.16 87.1 0.08 0.082 0.999 0.286 25.8 41276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 80.6 1.586 1.617 0.906 0.023 26.4
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 5Z3A 1.803 47.156 41275 2053 87.078 0.177 0.1758 0.1857 0.2061 0.2171 30.327
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] -0.334 -0.334 0.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.246 r_dihedral_angle_4_deg 18.031 r_dihedral_angle_3_deg 12.196 r_dihedral_angle_1_deg 6.022 r_lrange_it 5.638 r_lrange_other 5.615 r_scangle_it 4.632 r_scangle_other 4.631 r_scbond_it 3.384 r_scbond_other 3.355
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.246 r_dihedral_angle_4_deg 18.031 r_dihedral_angle_3_deg 12.196 r_dihedral_angle_1_deg 6.022 r_lrange_it 5.638 r_lrange_other 5.615 r_scangle_it 4.632 r_scangle_other 4.631 r_scbond_it 3.384 r_scbond_other 3.355 r_mcangle_it 3.29 r_mcangle_other 3.29 r_mcbond_it 2.64 r_mcbond_other 2.632 r_angle_refined_deg 1.678 r_angle_other_deg 1.53 r_chiral_restr_other 0.276 r_nbd_refined 0.227 r_nbd_other 0.188 r_symmetry_nbd_other 0.176 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.117 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2857 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing