3QP2

Crystal structure of CviR ligand-binding domain bound to C8-HSL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QP1PDB ENTRY 3QP1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION9296100 mM Tris-Cl, 200 mM magnesium chloride, 25-35% w/v PEG3350, pH 9.0, VAPOR DIFFUSION, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.3948.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.58α = 90
b = 55.907β = 90
c = 124.988γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 3152009-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

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
11.63862.49499.50.060.08415.95.8243942419122
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)
1.641.799.50.4982.194

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3QP11.63833.4072419123404119796.050.20170.20060.2227RANDOM
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]
-0.35373.4741-3.1204
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.962
f_angle_d1.076
f_chiral_restr0.069
f_bond_d0.006
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1403
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms16

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling