3H76

Crystal structure of PqsD, a key enzyme in Pseudomonas aeruginosa quinolone signal biosynthesis pathway


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HN9PDB entry 1HN9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.16 M MgCl2, 0.08M Tris-HCl pH 8.5, 24% PEG 4000, 20% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9436.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.081α = 90
b = 90.42β = 95.38
c = 67.894γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2008-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.82791.40.0915.13.149952
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)
1.81.8688.30.511.63.07

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1HN91.825.647404252891.380.201670.198220.26593RANDOM34.725
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]
0.51-0.18-0.12-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.467
r_dihedral_angle_4_deg19.042
r_dihedral_angle_3_deg16.97
r_sphericity_free9.156
r_dihedral_angle_1_deg7.401
r_sphericity_bonded4.382
r_scangle_it4.236
r_scbond_it3.03
r_rigid_bond_restr2.031
r_mcangle_it1.926
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.467
r_dihedral_angle_4_deg19.042
r_dihedral_angle_3_deg16.97
r_sphericity_free9.156
r_dihedral_angle_1_deg7.401
r_sphericity_bonded4.382
r_scangle_it4.236
r_scbond_it3.03
r_rigid_bond_restr2.031
r_mcangle_it1.926
r_angle_refined_deg1.913
r_mcbond_it1.312
r_symmetry_vdw_refined0.313
r_nbtor_refined0.306
r_xyhbond_nbd_refined0.259
r_nbd_refined0.241
r_symmetry_hbond_refined0.238
r_chiral_restr0.128
r_bond_refined_d0.018
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5007
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling