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Crystal structure of the Actinobacillus minor NM305 glucosyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-B3H2N1-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES pH 6.5, 0.2 M sodium formate, 14% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.592 α = 90 b = 44.312 β = 113.745 c = 90.754 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 6M 2022-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 1.85 50 98.9 0.02 0.998 38.7 1.9 29001
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 1.85 1.89 0.099 0.885
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 AlphaFold(AF-B3H2N1-F1) 1.85 46.487 29000 1425 98.787 0.159 0.1563 0.1563 0.2111 0.2106 11.551
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] 1.41 0.292 -2.078 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.081 r_dihedral_angle_3_deg 14.545 r_dihedral_angle_2_deg 9.279 r_dihedral_angle_1_deg 6.481 r_rigid_bond_restr 3.376 r_lrange_it 2.133 r_lrange_other 2.024 r_angle_refined_deg 1.466 r_scangle_it 1.159 r_scangle_other 1.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.081 r_dihedral_angle_3_deg 14.545 r_dihedral_angle_2_deg 9.279 r_dihedral_angle_1_deg 6.481 r_rigid_bond_restr 3.376 r_lrange_it 2.133 r_lrange_other 2.024 r_angle_refined_deg 1.466 r_scangle_it 1.159 r_scangle_other 1.159 r_mcangle_it 1.026 r_mcangle_other 1.026 r_scbond_it 0.845 r_scbond_other 0.845 r_mcbond_it 0.645 r_mcbond_other 0.645 r_angle_other_deg 0.5 r_nbd_refined 0.219 r_symmetry_nbd_refined 0.216 r_nbd_other 0.21 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.179 r_xyhbond_nbd_refined 0.149 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.022 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2779 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing