☰ Navigation Tabs
Structure of Rib domain from surface adhesin of Limosilactobacillus reuteri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.01M ZnSO4, 0.1M MES pH 6.5, 20% PEGMME 550, protein is premixed with 3mM CuCl2
Crystal Properties Matthews coefficient Solvent content 2.3 46.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.274 α = 90 b = 76.274 β = 90 c = 23.326 γ = 120
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 2022-09-24 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 1.35 19.91 99.7 0.061 20.2 8.3 17478
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 1.35 1.45 0.4
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 1.35 19.91 16600 851 99.61 0.12901 0.127 0.1325 0.16725 0.1726 RANDOM 10.356
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] 0.04 0.02 0.04 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.584 r_dihedral_angle_1_deg 6.569 r_long_range_B_refined 4.061 r_long_range_B_other 3.181 r_scbond_other 3.1 r_scangle_other 3.088 r_scbond_it 2.814 r_rigid_bond_restr 2.733 r_mcangle_other 2.073 r_mcangle_it 2.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.584 r_dihedral_angle_1_deg 6.569 r_long_range_B_refined 4.061 r_long_range_B_other 3.181 r_scbond_other 3.1 r_scangle_other 3.088 r_scbond_it 2.814 r_rigid_bond_restr 2.733 r_mcangle_other 2.073 r_mcangle_it 2.065 r_mcbond_other 1.596 r_mcbond_it 1.579 r_angle_refined_deg 1.438 r_angle_other_deg 0.476 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_2_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 595 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SADABS data reduction PHASER phasing