5E1Z

Crystal structure of the organohalide sensing RdhR-CbdbA1625 transcriptional regulator in the 2,4-dichlorophenol bound form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E1W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277Crystals formed in 0.1M Tris pH 7.5, 0.3M sodium acetate, 15% w/v PEG 4K were flash-cooled in liquid nitrogen by supplementing the mother liquor with 10% PEG 200.
Crystal Properties
Matthews coefficientSolvent content
3.0960.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.66α = 90
b = 71.66β = 90
c = 87.52γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.987DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.6650.6299.90.05823.59.829465
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)
11.661.7199.90.6823.39.7

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5E1W1.6650.6229465156499.910.182250.18080.21066RANDOM23.884
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]
0.520.260.52-1.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.977
r_dihedral_angle_4_deg23.023
r_dihedral_angle_3_deg14.279
r_long_range_B_refined5.895
r_dihedral_angle_1_deg5.233
r_scbond_it3.648
r_mcangle_it3.028
r_angle_refined_deg2.429
r_mcbond_it2.129
r_chiral_restr0.194
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.977
r_dihedral_angle_4_deg23.023
r_dihedral_angle_3_deg14.279
r_long_range_B_refined5.895
r_dihedral_angle_1_deg5.233
r_scbond_it3.648
r_mcangle_it3.028
r_angle_refined_deg2.429
r_mcbond_it2.129
r_chiral_restr0.194
r_bond_refined_d0.026
r_gen_planes_refined0.014
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 Atoms1378
Nucleic Acid Atoms
Solvent Atoms164
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing