5W43

Structure of the two-component response regulator RcsB-DNA complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52920.1 M Tris-HCl, 0.2 M ammonuim acetate, 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.8757.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.691α = 90
b = 121.691β = 90
c = 78.863γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2017-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
13.153099.90.090.715.24.911611
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.153.21000.824.9

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 REPLACEMENTTHROUGHOUTPDB entries 5I4C & 1JE83.15301101158199.670.186480.183190.25133RANDOM121.88
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]
0.750.370.75-2.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg47.421
r_dihedral_angle_3_deg24.846
r_dihedral_angle_4_deg21.342
r_long_range_B_refined11.955
r_dihedral_angle_1_deg7.154
r_mcangle_it5.647
r_scbond_it4.262
r_mcbond_it3.471
r_angle_refined_deg2.019
r_chiral_restr0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg47.421
r_dihedral_angle_3_deg24.846
r_dihedral_angle_4_deg21.342
r_long_range_B_refined11.955
r_dihedral_angle_1_deg7.154
r_mcangle_it5.647
r_scbond_it4.262
r_mcbond_it3.471
r_angle_refined_deg2.019
r_chiral_restr0.132
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3074
Nucleic Acid Atoms896
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
HKL-2000data reduction