3QP1

Crystal structure of CviR ligand-binding domain bound to the native ligand C6-HSL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QP6PDB ENTRY 3QP6

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
2.3948.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.543α = 90
b = 55.973β = 90
c = 125.223γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 3152010-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.5562.622960.04611288922817322
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)
1.551.61960.4762.5367.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 3QP61.5562.622817326749142397.510.216810.216810.215190.24735RANDOM29.393
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]
0.210.51-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.671
r_dihedral_angle_4_deg13.002
r_dihedral_angle_3_deg12.935
r_dihedral_angle_1_deg4.566
r_scangle_it3.567
r_scbond_it2.279
r_mcangle_it1.666
r_angle_refined_deg1.234
r_mcbond_it1.034
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.671
r_dihedral_angle_4_deg13.002
r_dihedral_angle_3_deg12.935
r_dihedral_angle_1_deg4.566
r_scangle_it3.567
r_scbond_it2.279
r_mcangle_it1.666
r_angle_refined_deg1.234
r_mcbond_it1.034
r_nbtor_refined0.305
r_symmetry_hbond_refined0.267
r_symmetry_vdw_refined0.237
r_nbd_refined0.211
r_xyhbond_nbd_refined0.178
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1403
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms14

Software

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