3SZT

Quorum Sensing Control Repressor, QscR, Bound to N-3-oxo-dodecanoyl-L-Homoserine Lactone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSCRWL MODEL OF AHL AND DNA-BINDING DOMAINS OF TRAR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.832770.168 M magnesium acetate, 21.8% PEG8000, 0.1 M Tris, pH 7.83, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.550.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.862α = 90
b = 94.862β = 90
c = 104.953γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12009-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.0000ALS4.2.2

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
12.5251000.0520.0524011.9192301923061.9
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)
12.52.5999.60.414.812.21882

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSCRWL MODEL OF AHL AND DNA-BINDING DOMAINS OF TRAR2.5515171161711695399.580.22490.22490.222640.26594RANDOM78.553
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]
-0.39-0.19-0.390.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.967
r_dihedral_angle_4_deg15.115
r_dihedral_angle_3_deg13.946
r_dihedral_angle_1_deg4.14
r_mcangle_it2.416
r_scangle_it1.621
r_mcbond_it1.573
r_angle_refined_deg1.295
r_scbond_it1.117
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.967
r_dihedral_angle_4_deg15.115
r_dihedral_angle_3_deg13.946
r_dihedral_angle_1_deg4.14
r_mcangle_it2.416
r_scangle_it1.621
r_mcbond_it1.573
r_angle_refined_deg1.295
r_scbond_it1.117
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3608
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms43

Software

Software
Software NamePurpose
Blu-Icedata collection
JBluIce-EPICSdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling