5O8Z

Conformational dynamism for DNA interaction in Salmonella typhimurium RcsB response regulator.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1A04 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29429% Jeffamine ED2003 0.1M lithium sulfate Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.0539.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.392α = 62.6
b = 54.266β = 81.61
c = 54.986γ = 79.66
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97947ALBAXALOC

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.148.6997.80.070.0820.03116.47.121487
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)RedundancyNumber Unique Reflections (All)
12.12.1696.40.8511.0040.377.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1A042.148.6920461102697.810.215450.213030.26542RANDOM47.953
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]
-2.15-0.121.290.9-0.30.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.049
r_dihedral_angle_4_deg21.284
r_dihedral_angle_3_deg16.583
r_dihedral_angle_1_deg5.427
r_long_range_B_refined4.321
r_long_range_B_other4.303
r_mcangle_it2.274
r_mcangle_other2.274
r_scangle_other1.863
r_angle_refined_deg1.367
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.049
r_dihedral_angle_4_deg21.284
r_dihedral_angle_3_deg16.583
r_dihedral_angle_1_deg5.427
r_long_range_B_refined4.321
r_long_range_B_other4.303
r_mcangle_it2.274
r_mcangle_other2.274
r_scangle_other1.863
r_angle_refined_deg1.367
r_mcbond_it1.298
r_mcbond_other1.294
r_scbond_other1.072
r_scbond_it1.071
r_angle_other_deg0.936
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms3045
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing