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Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in a closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VEV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG3350
0.2 M Ammonium formate
0.0209 mM Polygalacturonic acid sodium
Crystal Properties Matthews coefficient Solvent content 2.16 43.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.626 α = 103.034 b = 54.998 β = 97.4 c = 112.829 γ = 92.36
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 4M 2021-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1 SPring-8 BL26B1
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 2.25 48.2 95.9 0.055 14.2 6.12 53456
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 2.25 2.39 0.109
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7VEV 2.25 43.53 53456 2673 95.957 0.211 0.2089 0.2072 0.2512 0.2519 28.387
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] -0.471 -1.812 -0.299 -2.102 0.29 2.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.332 r_dihedral_angle_4_deg 14.146 r_dihedral_angle_3_deg 13.111 r_lrange_other 6.318 r_lrange_it 6.314 r_scangle_it 6.289 r_scangle_other 6.289 r_dihedral_angle_1_deg 6.204 r_scbond_it 5.593 r_scbond_other 5.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.332 r_dihedral_angle_4_deg 14.146 r_dihedral_angle_3_deg 13.111 r_lrange_other 6.318 r_lrange_it 6.314 r_scangle_it 6.289 r_scangle_other 6.289 r_dihedral_angle_1_deg 6.204 r_scbond_it 5.593 r_scbond_other 5.592 r_mcangle_it 5.011 r_mcangle_other 5.011 r_mcbond_it 4.301 r_mcbond_other 4.301 r_angle_other_deg 2.24 r_angle_refined_deg 1.79 r_nbd_other 0.32 r_symmetry_nbd_other 0.222 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.206 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.153 r_symmetry_xyhbond_nbd_other 0.13 r_xyhbond_nbd_other 0.129 r_symmetry_nbd_refined 0.116 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.074 r_bond_other_d 0.034 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9692 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing