3H78

Crystal structure of Pseudomonas aeruginosa PqsD C112A mutant in complex with anthranilic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H77PDB entry 3H77

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
1.9637.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.465α = 90
b = 59.178β = 92.3
c = 125.993γ = 90
Symmetry
Space GroupC 1 2 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
11.75093.70.0617.86.562039
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)
1.71.7684.10.3877.15.8

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 3H771.74058860316393.580.152380.15010.19535RANDOM17.183
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]
0.010.01-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.214
r_dihedral_angle_4_deg18.964
r_dihedral_angle_3_deg12.222
r_dihedral_angle_1_deg5.466
r_sphericity_free3.593
r_scangle_it2.913
r_sphericity_bonded2.369
r_scbond_it1.993
r_angle_refined_deg1.337
r_mcangle_it1.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.214
r_dihedral_angle_4_deg18.964
r_dihedral_angle_3_deg12.222
r_dihedral_angle_1_deg5.466
r_sphericity_free3.593
r_scangle_it2.913
r_sphericity_bonded2.369
r_scbond_it1.993
r_angle_refined_deg1.337
r_mcangle_it1.3
r_rigid_bond_restr1.276
r_mcbond_it1.018
r_nbtor_refined0.301
r_nbd_refined0.206
r_symmetry_hbond_refined0.191
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.139
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5119
Nucleic Acid Atoms
Solvent Atoms655
Heterogen Atoms30

Software

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