3CNV

Crystal structure of the ligand-binding domain of a putative GntR-family transcriptional regulator from Bordetella bronchiseptica


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72730.1M Bis-tris pH 7.0, 1M Tri-ammonium citrate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K
Crystal Properties
Matthews coefficientSolvent content
2.7755.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.196α = 82.36
b = 58.071β = 86.52
c = 65.58γ = 68.31
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPS-1Mirrors2008-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97934APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
125097.60.1220.12218.3874.15260452604-334
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0395.80.3820.38233

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT229.91515915159126140.1670.1670.1640.217RANDOM16.59
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]
1.20.56-0.84-1.910.530.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.955
r_dihedral_angle_4_deg18.243
r_dihedral_angle_3_deg14.767
r_dihedral_angle_1_deg7.012
r_scangle_it5.404
r_scbond_it3.367
r_mcangle_it2.102
r_angle_refined_deg1.922
r_angle_other_deg1.44
r_mcbond_it1.162
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.955
r_dihedral_angle_4_deg18.243
r_dihedral_angle_3_deg14.767
r_dihedral_angle_1_deg7.012
r_scangle_it5.404
r_scbond_it3.367
r_mcangle_it2.102
r_angle_refined_deg1.922
r_angle_other_deg1.44
r_mcbond_it1.162
r_mcbond_other0.339
r_chiral_restr0.113
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4999
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms57

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-2000data reduction
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
REFMACrefinement
HKL-3000data reduction
HKL-2000data scaling
DMphasing