3H77

Crystal structure of Pseudomonas aeruginosa PqsD in a covalent complex with anthranilate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H76PDB entry 3H76

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52930.2 M MgCl2, 0.1M Tris-HCl pH 8.5, 21% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.894α = 90
b = 59.656β = 103.95
c = 83.427γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

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
11.85099.70.0687.8759980
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)
1.81.8699.30.4026.26.1

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 3H761.83056914302699.630.154090.151860.19488RANDOM25.632
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]
-0.060.060.16-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.851
r_dihedral_angle_4_deg17.561
r_dihedral_angle_3_deg13.973
r_dihedral_angle_1_deg6.796
r_sphericity_free4.501
r_scangle_it3.401
r_scbond_it3.074
r_rigid_bond_restr2.897
r_sphericity_bonded2.82
r_angle_refined_deg1.663
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.851
r_dihedral_angle_4_deg17.561
r_dihedral_angle_3_deg13.973
r_dihedral_angle_1_deg6.796
r_sphericity_free4.501
r_scangle_it3.401
r_scbond_it3.074
r_rigid_bond_restr2.897
r_sphericity_bonded2.82
r_angle_refined_deg1.663
r_mcangle_it1.46
r_mcbond_it1.15
r_nbtor_refined0.305
r_nbd_refined0.228
r_symmetry_vdw_refined0.213
r_symmetry_hbond_refined0.181
r_xyhbond_nbd_refined0.149
r_chiral_restr0.142
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5160
Nucleic Acid Atoms
Solvent Atoms582
Heterogen Atoms114

Software

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