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Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with galacturonic acid
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 5.5 293 40% PEG600
0.1 M Citrate
50 mM Galacturonic acid sodium
Crystal Properties Matthews coefficient Solvent content 2.19 43.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.686 α = 90 b = 86.662 β = 90 c = 97.323 γ = 90
Symmetry Space Group P 21 21 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 2021-02-14 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 1.736 42.4 99.3 0.068 25.6 6.17 63700
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 1.74 1.84 0.529
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7VEV 1.736 40.436 63700 3185 99.257 0.157 0.1557 0.1812 0.185 18.611
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] 0.877 -1.128 0.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.914 r_dihedral_angle_4_deg 13.052 r_dihedral_angle_3_deg 12.777 r_dihedral_angle_1_deg 6.325 r_lrange_it 5.827 r_lrange_other 5.813 r_scangle_it 5.645 r_scangle_other 5.645 r_scbond_it 4.281 r_scbond_other 4.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.914 r_dihedral_angle_4_deg 13.052 r_dihedral_angle_3_deg 12.777 r_dihedral_angle_1_deg 6.325 r_lrange_it 5.827 r_lrange_other 5.813 r_scangle_it 5.645 r_scangle_other 5.645 r_scbond_it 4.281 r_scbond_other 4.28 r_mcangle_other 3.021 r_mcangle_it 3.02 r_mcbond_it 2.456 r_mcbond_other 2.452 r_angle_other_deg 2.223 r_angle_refined_deg 1.72 r_nbd_other 0.274 r_nbd_refined 0.225 r_symmetry_nbd_other 0.217 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.146 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.097 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.075 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 4872 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing