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Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with noncovalent Cyclophellitol Sulfamidate probe KK131
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 2% PEG400
Crystal Properties Matthews coefficient Solvent content 3.02 59.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197 α = 90 b = 197 β = 90 c = 102.156 γ = 120
Symmetry Space Group P 6 2 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 PILATUS 6M-F 2019-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 1.86 102.31 100 0.124 0.127 0.025 0.999 14.5 24.6 97555 35.281
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 1.86 1.89 2.839 2.9 0.589 0.618 1.3
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 4b9y 1.86 102.31 97548 4828 99.965 0.193 0.1915 0.1896 0.229 0.2277 41.32
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] -1.361 -0.68 -1.361 4.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.562 r_dihedral_angle_4_deg 16.929 r_dihedral_angle_3_deg 13.814 r_dihedral_angle_1_deg 7.717 r_lrange_other 7.704 r_lrange_it 7.703 r_scangle_it 6.36 r_scangle_other 6.24 r_mcangle_it 4.636 r_mcangle_other 4.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.562 r_dihedral_angle_4_deg 16.929 r_dihedral_angle_3_deg 13.814 r_dihedral_angle_1_deg 7.717 r_lrange_other 7.704 r_lrange_it 7.703 r_scangle_it 6.36 r_scangle_other 6.24 r_mcangle_it 4.636 r_mcangle_other 4.636 r_scbond_it 4.257 r_scbond_other 4.166 r_mcbond_it 3.516 r_mcbond_other 3.516 r_angle_other_deg 2.334 r_angle_refined_deg 1.603 r_chiral_restr_other 1.337 r_nbd_other 0.226 r_symmetry_nbd_other 0.216 r_nbd_refined 0.197 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.153 r_symmetry_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.152 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.07 r_bond_other_d 0.035 r_gen_planes_other 0.013 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6237 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing