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Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 29% Jeffamine ED2003
0.1M lithium sulfate
Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.05 39.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.392 α = 62.6 b = 54.266 β = 81.61 c = 54.986 γ = 79.66
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 2015-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97947 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 48.69 97.8 0.07 0.082 0.031 16.4 7.1 21487
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 96.4 0.851 1.004 0.37 7.2
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 1A04 2.1 48.69 20461 1026 97.81 0.21545 0.21303 0.2164 0.26542 0.2713 RANDOM 47.953
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] -2.15 -0.12 1.29 0.9 -0.3 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.049 r_dihedral_angle_4_deg 21.284 r_dihedral_angle_3_deg 16.583 r_dihedral_angle_1_deg 5.427 r_long_range_B_refined 4.321 r_long_range_B_other 4.303 r_mcangle_it 2.274 r_mcangle_other 2.274 r_scangle_other 1.863 r_angle_refined_deg 1.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.049 r_dihedral_angle_4_deg 21.284 r_dihedral_angle_3_deg 16.583 r_dihedral_angle_1_deg 5.427 r_long_range_B_refined 4.321 r_long_range_B_other 4.303 r_mcangle_it 2.274 r_mcangle_other 2.274 r_scangle_other 1.863 r_angle_refined_deg 1.367 r_mcbond_it 1.298 r_mcbond_other 1.294 r_scbond_other 1.072 r_scbond_it 1.071 r_angle_other_deg 0.936 r_chiral_restr 0.072 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 3045 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing