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Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with Cyclophellitol Aziridine probe CF021
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 7 293 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH7.0), 2% PEG400
Crystal Properties Matthews coefficient Solvent content 3.06 59.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.3 α = 90 b = 197.3 β = 90 c = 102.9 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 2016-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 170.87 100 0.097 26.8 24.5 100134
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 100 1.21 3 25
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4B9Y 1.85 170.87 95234 4899 99.99 0.17002 0.16905 0.179 0.18813 0.1955 RANDOM 34.16
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] -0.45 -0.23 -0.45 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.374 r_dihedral_angle_4_deg 15.944 r_dihedral_angle_3_deg 13.101 r_dihedral_angle_1_deg 6.597 r_long_range_B_refined 6.204 r_long_range_B_other 6.197 r_scangle_other 2.013 r_angle_refined_deg 1.583 r_scbond_it 1.229 r_scbond_other 1.225
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.374 r_dihedral_angle_4_deg 15.944 r_dihedral_angle_3_deg 13.101 r_dihedral_angle_1_deg 6.597 r_long_range_B_refined 6.204 r_long_range_B_other 6.197 r_scangle_other 2.013 r_angle_refined_deg 1.583 r_scbond_it 1.229 r_scbond_other 1.225 r_mcangle_it 1.201 r_mcangle_other 1.201 r_angle_other_deg 0.976 r_mcbond_it 0.754 r_mcbond_other 0.747 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6229 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing