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Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in an open 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 8.5 293 2.0 M Ammonium dihydrogenphosphate
0.1 M Tris-HCl
2.0 mM Unsaturated trigalacturonic acid
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.855 α = 90 b = 151.663 β = 90 c = 179.52 γ = 90
Symmetry Space Group C 2 2 21
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 2020-10-24 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 1.696 48.217 97.8 0.086 11.1 5.02 76813
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 1.7 1.74 0.555 1.87
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 1.696 48.217 76813 3841 99.491 0.169 0.1677 0.1751 0.195 0.2063 19.515
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] -0.247 -0.819 1.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_dihedral_angle_3_deg 11.632 r_dihedral_angle_4_deg 11.052 r_dihedral_angle_1_deg 6.267 r_lrange_it 5.985 r_lrange_other 5.954 r_scangle_it 5.572 r_scangle_other 5.571 r_scbond_it 4.322 r_scbond_other 4.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_dihedral_angle_3_deg 11.632 r_dihedral_angle_4_deg 11.052 r_dihedral_angle_1_deg 6.267 r_lrange_it 5.985 r_lrange_other 5.954 r_scangle_it 5.572 r_scangle_other 5.571 r_scbond_it 4.322 r_scbond_other 4.321 r_mcangle_other 3.411 r_mcangle_it 3.399 r_mcbond_it 2.805 r_mcbond_other 2.785 r_angle_other_deg 2.224 r_angle_refined_deg 1.707 r_nbd_other 0.281 r_symmetry_xyhbond_nbd_refined 0.234 r_nbd_refined 0.225 r_symmetry_nbd_other 0.218 r_nbtor_refined 0.186 r_symmetry_nbd_refined 0.163 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.039 r_bond_other_d 0.034 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4846 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing