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Limosilactobacillus reuteri N1 GtfB-acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 4% v/v MPD, 0.1 M Citric acid pH 3.5, 20% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.83 56.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.77 α = 90 b = 100.62 β = 108.17 c = 106.67 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 Bruker PHOTON II 2022-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54178
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 2.66 47.11 99 0.099 7.2 2.9 58618
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 2.66 2.73 0.501
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 (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 2.66 47.11 55652 2965 98.98 0.21456 0.21205 0.2192 0.26217 0.2639 RANDOM 35.109
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] 3.87 0.28 0.31 -3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.881 r_dihedral_angle_4_deg 15.777 r_dihedral_angle_3_deg 15.277 r_dihedral_angle_1_deg 6.55 r_long_range_B_refined 5.725 r_long_range_B_other 5.687 r_mcangle_it 3.097 r_mcangle_other 3.097 r_scangle_other 3.002 r_mcbond_it 1.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.881 r_dihedral_angle_4_deg 15.777 r_dihedral_angle_3_deg 15.277 r_dihedral_angle_1_deg 6.55 r_long_range_B_refined 5.725 r_long_range_B_other 5.687 r_mcangle_it 3.097 r_mcangle_other 3.097 r_scangle_other 3.002 r_mcbond_it 1.828 r_mcbond_other 1.828 r_scbond_it 1.82 r_scbond_other 1.82 r_angle_refined_deg 1.307 r_angle_other_deg 0.785 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 12914 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing