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Structure of trehalose bound Alistipes sp. Glucoside-3-dehydrogenase AL3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.25 M Sodium Malonate
17% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.74 55.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.581 α = 90 b = 57.221 β = 106.584 c = 224.962 γ = 90
Symmetry Space Group I 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 9M 2023-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0332 APS 21-ID-D
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 2.95 162.27 89.9 0.141 0.199 0.141 0.95 3.5 2.7 43707
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 2.95 3.06 0.462 0.654 0.462 0.497 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.95 162.267 43706 2195 89.655 0.198 0.1949 0.2056 0.2471 0.2471 RANDOM 40.815
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] -3.91 1.823 -1.193 3.412
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.604 r_dihedral_angle_6_deg 14.774 r_dihedral_angle_2_deg 10.348 r_dihedral_angle_1_deg 7.848 r_angle_refined_deg 5.641 r_lrange_it 3.573 r_lrange_other 3.562 r_scangle_it 2.453 r_scangle_other 2.453 r_scbond_it 1.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.604 r_dihedral_angle_6_deg 14.774 r_dihedral_angle_2_deg 10.348 r_dihedral_angle_1_deg 7.848 r_angle_refined_deg 5.641 r_lrange_it 3.573 r_lrange_other 3.562 r_scangle_it 2.453 r_scangle_other 2.453 r_scbond_it 1.428 r_scbond_other 1.428 r_dihedral_angle_other_2_deg 0.947 r_mcangle_it 0.789 r_mcangle_other 0.789 r_angle_other_deg 0.682 r_mcbond_it 0.436 r_mcbond_other 0.436 r_nbd_other 0.228 r_nbd_refined 0.223 r_symmetry_nbd_other 0.213 r_symmetry_xyhbond_nbd_refined 0.208 r_nbtor_refined 0.195 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_refined 0.188 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.09 r_ncsr_local_group_3 0.075 r_ncsr_local_group_4 0.075 r_ncsr_local_group_5 0.075 r_ncsr_local_group_1 0.074 r_ncsr_local_group_2 0.073 r_ncsr_local_group_6 0.071 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.011 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 14208 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 682
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing