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Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with 1-deoxynojirimycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 300 mM ammonium citrate, pH 7.0-8.0, 10 mM TCEP, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.841 α = 90 b = 194.371 β = 116.541 c = 112.129 γ = 90
Symmetry Space Group C 1 2 1
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 2021-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
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 1.9 48.64 99.9 0.099 0.997 10.5 6.7 184040
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 1.9 1.93 0.498 0.944 3.1
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 48.64 183351 9198 99.543 0.255 0.2539 0.2615 0.2762 0.2822 39.476
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] -0.778 0.554 -2.402 1.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.556 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_2_deg 7.37 r_dihedral_angle_1_deg 6.979 r_lrange_it 5.139 r_lrange_other 5.117 r_scangle_it 1.947 r_scangle_other 1.947 r_mcangle_it 1.549 r_mcangle_other 1.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.556 r_dihedral_angle_3_deg 13.129 r_dihedral_angle_2_deg 7.37 r_dihedral_angle_1_deg 6.979 r_lrange_it 5.139 r_lrange_other 5.117 r_scangle_it 1.947 r_scangle_other 1.947 r_mcangle_it 1.549 r_mcangle_other 1.549 r_angle_refined_deg 1.483 r_scbond_it 1.208 r_scbond_other 1.208 r_mcbond_it 0.969 r_mcbond_other 0.969 r_angle_other_deg 0.516 r_nbd_refined 0.211 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.186 r_symmetry_nbd_refined 0.183 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.166 r_nbd_other 0.149 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.077 r_ncsr_local_group_1 0.062 r_ncsr_local_group_2 0.06 r_ncsr_local_group_3 0.051 r_symmetry_xyhbond_nbd_other 0.041 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15741 Nucleic Acid Atoms Solvent Atoms 886 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing