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Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator. S207C P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O8Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 16 % PEG4000, 0.2 M lithium sulfate and Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.1 41.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.621 α = 90 b = 74.222 β = 90 c = 75.213 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 PILATUS3 S 6M 2017-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.5 75.2 100 0.067 0.072 0.027 0.999 17.7 6.8 14033
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 100 0.653 0.718 0.295 0.817 2.7 5.9 1541
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5O8Y 2.5 52.83 13288 701 99.96 0.21795 0.21513 0.2187 0.26898 0.2797 RANDOM 58.915
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] -0.5 -3.5 4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_3_deg 16.118 r_dihedral_angle_4_deg 16.071 r_long_range_B_other 5.456 r_long_range_B_refined 5.455 r_dihedral_angle_1_deg 5.232 r_mcangle_it 3.245 r_mcangle_other 3.244 r_scangle_other 3.197 r_mcbond_it 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.496 r_dihedral_angle_3_deg 16.118 r_dihedral_angle_4_deg 16.071 r_long_range_B_other 5.456 r_long_range_B_refined 5.455 r_dihedral_angle_1_deg 5.232 r_mcangle_it 3.245 r_mcangle_other 3.244 r_scangle_other 3.197 r_mcbond_it 1.97 r_mcbond_other 1.966 r_scbond_it 1.92 r_scbond_other 1.897 r_angle_refined_deg 1.098 r_angle_other_deg 0.744 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_bond_other_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3051 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing