2HJ9 | pdb_00002hj9

Crystal structure of the Autoinducer-2-bound form of Vibrio harveyi LuxP complexed with the periplasmic domain of LuxQ


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2961:1 mixture of protein (20 mg/ml in 20 mM Tris-HCl (pH 7.5), 150 mM NaCl) and well solution (27.5% (w/v) PEG 400, 100 mM potassium nitrate, 100 mM 2-morpholinoethanesulfonic acid monohydrate (pH 6.0), 100 M 4,5-dihydroxy-2,3-pentane dione, and 1 mM boric acid), VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.5151.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.916α = 90
b = 83.916β = 90
c = 365.328γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.343098.155573
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.342.4296.5

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.3429.75272852723282798.390.209660.206890.210.261780.26RANDOM55.523
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]
0.760.76-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.19
r_dihedral_angle_4_deg17.858
r_dihedral_angle_3_deg17.414
r_dihedral_angle_1_deg6.238
r_scangle_it2.775
r_scbond_it1.764
r_angle_refined_deg1.458
r_mcangle_it1.302
r_mcbond_it0.726
r_nbtor_refined0.304
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8674
Nucleic Acid Atoms
Solvent Atoms394
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing