☰ Navigation Tabs
Crystal structure of bacterial chemotaxis-dependent pectin-binding protein SPH1118 in complex with unsaturated trigalacturonic 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 7.2 293 22% PEG3000
0.15 M Potassium sodium tartrate
0.1 M HEPES
23.4 mM Unsaturated trigalacturonic acid
Crystal Properties Matthews coefficient Solvent content 2.51 51.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.687 α = 90 b = 83.657 β = 101.036 c = 148.521 γ = 90
Symmetry Space Group P 1 21 1
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 1.9 48.6 99.5 0.086 11.3 5.77 108404
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 1.9 2.02 0.645
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 1.92 48.591 105761 5288 99.894 0.211 0.2096 0.2117 0.2324 0.2364 34.749
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] 5.528 1.119 -3.394 -2.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.885 r_dihedral_angle_4_deg 13.681 r_dihedral_angle_3_deg 12.902 r_dihedral_angle_1_deg 6.282 r_lrange_other 3.752 r_lrange_it 3.75 r_scangle_it 3.509 r_scangle_other 3.509 r_scbond_it 2.757 r_scbond_other 2.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.885 r_dihedral_angle_4_deg 13.681 r_dihedral_angle_3_deg 12.902 r_dihedral_angle_1_deg 6.282 r_lrange_other 3.752 r_lrange_it 3.75 r_scangle_it 3.509 r_scangle_other 3.509 r_scbond_it 2.757 r_scbond_other 2.756 r_mcangle_other 2.405 r_mcangle_it 2.402 r_angle_other_deg 2.211 r_mcbond_it 1.966 r_mcbond_other 1.963 r_angle_refined_deg 1.73 r_nbd_other 0.373 r_nbd_refined 0.227 r_symmetry_nbd_other 0.222 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.165 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.098 r_symmetry_xyhbond_nbd_other 0.097 r_symmetry_xyhbond_nbd_refined 0.084 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.034 r_bond_refined_d 0.014 r_gen_planes_other 0.005 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9692 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing