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Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with covalent Cyclophellitol Sulfamidate probe KK130
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 3.24 62.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.076 α = 90 b = 197.076 β = 90 c = 102.149 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 1.85 98.54 100 0.133 0.136 0.027 0.999 14.2 24.7 99190
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 1.85 1.88 2.685 2.741 0.545 0.696 1.4
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 4b9y 1.85 98.538 99175 4583 99.947 0.19 0.1884 0.1865 0.2216 0.2197 39.213
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] -1.224 -0.612 -1.224 3.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.51 r_dihedral_angle_4_deg 16.169 r_dihedral_angle_3_deg 14.676 r_lrange_it 7.942 r_lrange_other 7.914 r_dihedral_angle_1_deg 7.687 r_scangle_it 6.377 r_scangle_other 6.263 r_mcangle_it 4.544 r_mcangle_other 4.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.51 r_dihedral_angle_4_deg 16.169 r_dihedral_angle_3_deg 14.676 r_lrange_it 7.942 r_lrange_other 7.914 r_dihedral_angle_1_deg 7.687 r_scangle_it 6.377 r_scangle_other 6.263 r_mcangle_it 4.544 r_mcangle_other 4.544 r_scbond_it 4.244 r_scbond_other 4.158 r_mcbond_it 3.438 r_mcbond_other 3.437 r_angle_other_deg 2.326 r_angle_refined_deg 1.62 r_chiral_restr_other 0.963 r_symmetry_nbd_other 0.217 r_nbd_other 0.211 r_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.195 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.157 r_symmetry_nbd_refined 0.146 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.078 r_bond_other_d 0.035 r_symmetry_xyhbond_nbd_other 0.032 r_gen_planes_other 0.014 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 485 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing