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Structure of long Rib domain from Limosilactobacillus reuteri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S5W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 2.4 M Na Malonate pH 7, 0.2 M NaSCN
Crystal Properties Matthews coefficient Solvent content 1.88 34.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.161 α = 90 b = 36.161 β = 90 c = 126.332 γ = 90
Symmetry Space Group P 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL Bruker PHOTON II 2021-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.54
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 1.46 23.8 95.4 0.059 20.2 6.4 14807
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 1.46 1.56 0.343
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 1.46 23.8 14016 734 95.41 0.15536 0.15388 0.1551 0.18257 0.1539 RANDOM 14.491
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.154 r_long_range_B_refined 12.188 r_long_range_B_other 10.519 r_dihedral_angle_1_deg 7.845 r_dihedral_angle_2_deg 6.637 r_scangle_other 2.452 r_mcangle_it 2.092 r_mcangle_other 2.091 r_scbond_it 1.711 r_angle_refined_deg 1.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.154 r_long_range_B_refined 12.188 r_long_range_B_other 10.519 r_dihedral_angle_1_deg 7.845 r_dihedral_angle_2_deg 6.637 r_scangle_other 2.452 r_mcangle_it 2.092 r_mcangle_other 2.091 r_scbond_it 1.711 r_angle_refined_deg 1.648 r_scbond_other 1.623 r_mcbond_it 1.294 r_mcbond_other 1.23 r_angle_other_deg 0.563 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 743 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SADABS data scaling SAINT data reduction PHASER phasing