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Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in a full 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 6.5 293 25% PEG550MME
0.1 M MES
0.01 M Zinc sulfate
0.0209 mM Polygalacturonic acid sodium
Crystal Properties Matthews coefficient Solvent content 2.18 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.961 α = 90 b = 84.727 β = 90 c = 90.025 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 2021-07-18 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 1.699 48.848 98.3 0.045 33.3 10.7 66777
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 1.8 0.253
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 1.699 48.848 66774 3339 98.278 0.181 0.1797 0.1836 0.2119 0.2171 20.438
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] 0.419 -2.279 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.498 r_dihedral_angle_4_deg 13.253 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_1_deg 6.122 r_lrange_it 4.771 r_lrange_other 4.721 r_scangle_it 4.58 r_scangle_other 4.579 r_scbond_it 3.655 r_scbond_other 3.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.498 r_dihedral_angle_4_deg 13.253 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_1_deg 6.122 r_lrange_it 4.771 r_lrange_other 4.721 r_scangle_it 4.58 r_scangle_other 4.579 r_scbond_it 3.655 r_scbond_other 3.654 r_mcangle_other 3.046 r_mcangle_it 3.036 r_mcbond_it 2.552 r_mcbond_other 2.533 r_angle_other_deg 2.223 r_angle_refined_deg 1.697 r_nbd_refined 0.223 r_symmetry_nbd_other 0.22 r_nbd_other 0.192 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.124 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.073 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 4851 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing