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Crystal structure of the Actinobacillus minor NM305 glucosyltransferase in complex with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XSH
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) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.136 α = 90 b = 43.39 β = 117.44 c = 95.823 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 EIGER X 16M 2022-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00003 SLS X06SA
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 1.8 50 96.7 0.034 1 33 7 32975
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 0.989
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 8XSH 1.8 42.557 32974 1696 96.339 0.161 0.1584 0.1586 0.2013 0.2017 28.179
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] 0.838 -0.585 -0.417 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.207 r_dihedral_angle_3_deg 13.248 r_dihedral_angle_2_deg 9.498 r_dihedral_angle_1_deg 6.804 r_lrange_it 4.11 r_lrange_other 4.019 r_rigid_bond_restr 3.981 r_scangle_it 3.21 r_scangle_other 3.21 r_mcangle_other 2.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.207 r_dihedral_angle_3_deg 13.248 r_dihedral_angle_2_deg 9.498 r_dihedral_angle_1_deg 6.804 r_lrange_it 4.11 r_lrange_other 4.019 r_rigid_bond_restr 3.981 r_scangle_it 3.21 r_scangle_other 3.21 r_mcangle_other 2.842 r_mcangle_it 2.837 r_scbond_it 2.317 r_scbond_other 2.315 r_mcbond_it 2.055 r_mcbond_other 2.046 r_angle_refined_deg 1.448 r_angle_other_deg 0.515 r_nbd_refined 0.217 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.187 r_symmetry_nbd_refined 0.186 r_xyhbond_nbd_refined 0.142 r_nbd_other 0.142 r_symmetry_xyhbond_nbd_refined 0.106 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2796 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing