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Limosilactobacillus reuteri N1 GtfB
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 56.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.42 α = 90 b = 100.73 β = 108.14 c = 106.89 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 150 PIXEL Bruker PHOTON II 2022-07-26 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 2.76 47.21 99.7 0.103 7.2 2.9 52935
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 2.76 2.84 0.348
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 2.76 47.21 50269 2666 99.6 0.24849 0.24755 0.2518 0.26609 0.2718 RANDOM 30.973
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] 3.43 0.6 -0.93 -2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.075 r_dihedral_angle_4_deg 13.496 r_dihedral_angle_3_deg 13.438 r_dihedral_angle_1_deg 6.054 r_long_range_B_refined 1.876 r_long_range_B_other 1.875 r_angle_refined_deg 1.18 r_angle_other_deg 1.054 r_mcangle_it 0.688 r_mcangle_other 0.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.075 r_dihedral_angle_4_deg 13.496 r_dihedral_angle_3_deg 13.438 r_dihedral_angle_1_deg 6.054 r_long_range_B_refined 1.876 r_long_range_B_other 1.875 r_angle_refined_deg 1.18 r_angle_other_deg 1.054 r_mcangle_it 0.688 r_mcangle_other 0.688 r_mcbond_it 0.359 r_mcbond_other 0.359 r_scangle_other 0.28 r_scbond_it 0.101 r_scbond_other 0.101 r_chiral_restr 0.031 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 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 86 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing