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Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with isomaltose
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 300mM ammonium citrate, pH 7.0-8.0, 10mM TCEP, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.61 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.938 α = 90 b = 194.09 β = 116.348 c = 111.88 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 PILATUS 2M 2021-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.56 48.54 98.2 0.072 0.088 0.049 0.999 13.2 6.1 326516
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 0.947 1.15 0.644 0.813 2
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 1.56 44.71 326232 16344 98.263 0.188 0.1873 0.1928 0.2114 0.2174 26.71
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] -2.046 1.149 -3.159 2.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.991 r_dihedral_angle_3_deg 14.994 r_dihedral_angle_2_deg 8.312 r_dihedral_angle_1_deg 7.063 r_lrange_it 5.342 r_lrange_other 5.315 r_scangle_it 3.648 r_scangle_other 3.648 r_scbond_it 2.501 r_scbond_other 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.991 r_dihedral_angle_3_deg 14.994 r_dihedral_angle_2_deg 8.312 r_dihedral_angle_1_deg 7.063 r_lrange_it 5.342 r_lrange_other 5.315 r_scangle_it 3.648 r_scangle_other 3.648 r_scbond_it 2.501 r_scbond_other 2.5 r_angle_refined_deg 1.974 r_mcangle_other 1.942 r_mcangle_it 1.941 r_mcbond_it 1.454 r_mcbond_other 1.454 r_angle_other_deg 0.673 r_nbd_refined 0.229 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.188 r_symmetry_nbd_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.161 r_nbd_other 0.155 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.107 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15741 Nucleic Acid Atoms Solvent Atoms 1414 Heterogen Atoms 189
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing