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The novel membrane-proximal sensing mechanism in a broad-ligand binding chemoreceptor McpA of Bacillus velezensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PXY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.17 M ammonium acetate, 0.085M sodium acetate pH 4.6, 25.5 % PEG 4000, 15 % glycerol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.161 α = 90 b = 32.855 β = 90 c = 57.903 γ = 90
Symmetry Space Group P 21 21 2
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 16M 2020-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
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 2.247 50 99.7 0.091 20.4 7.8 17195
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 2.29 0.477
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 THROUGHOUT 6pxy 2.247 48.756 17150 870 99.547 0.185 0.1825 0.1912 0.2367 0.2407 47.448
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] -0.827 -3.438 4.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.798 r_dihedral_angle_4_deg 17.591 r_dihedral_angle_3_deg 14.955 r_lrange_other 9.157 r_lrange_it 9.155 r_scangle_it 7.516 r_scangle_other 7.514 r_dihedral_angle_1_deg 6.83 r_mcangle_it 5.134 r_mcangle_other 5.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.798 r_dihedral_angle_4_deg 17.591 r_dihedral_angle_3_deg 14.955 r_lrange_other 9.157 r_lrange_it 9.155 r_scangle_it 7.516 r_scangle_other 7.514 r_dihedral_angle_1_deg 6.83 r_mcangle_it 5.134 r_mcangle_other 5.133 r_scbond_it 4.912 r_scbond_other 4.911 r_mcbond_it 3.744 r_mcbond_other 3.73 r_angle_refined_deg 1.47 r_angle_other_deg 1.276 r_nbd_refined 0.195 r_symmetry_xyhbond_nbd_refined 0.185 r_symmetry_nbd_other 0.17 r_nbd_other 0.166 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.15 r_ncsr_local_group_1 0.118 r_symmetry_nbd_refined 0.098 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2299 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing