3HGX

Crystal Structure of Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase K42A mutant in complex with salicylate and pyruvate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H9DPDB ENTRY 2H9D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291.150.1M Tris-HCl, pH 8.5, 2M ammonium phosphate, 13% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties
Matthews coefficientSolvent content
2.3447.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.015α = 90
b = 53.15β = 90
c = 82.336γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113.15IMAGE PLATERIGAKU RAXIS IV++2007-06-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.54

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
12.510099.90.10115.2346.67706
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)
2.52.5999.90.2776.7749

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 2H9D2.541.49734635099.750.2180.2160.276RANDOM15.597
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]
0.07-0.01-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.461
r_dihedral_angle_3_deg15.732
r_dihedral_angle_4_deg13.846
r_dihedral_angle_1_deg4.613
r_scangle_it1.879
r_angle_refined_deg1.219
r_scbond_it1.2
r_mcangle_it0.813
r_mcbond_it0.5
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.461
r_dihedral_angle_3_deg15.732
r_dihedral_angle_4_deg13.846
r_dihedral_angle_1_deg4.613
r_scangle_it1.879
r_angle_refined_deg1.219
r_scbond_it1.2
r_mcangle_it0.813
r_mcbond_it0.5
r_nbtor_refined0.299
r_nbd_refined0.194
r_symmetry_vdw_refined0.155
r_xyhbond_nbd_refined0.118
r_symmetry_hbond_refined0.114
r_chiral_restr0.094
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1578
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms32

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing