3RET

Salicylate and Pyruvate Bound Structure of the Isochorismate-Pyruvate Lyase K42E Mutant from Pseudomonas aerugionsa


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.62980.004 M gly-gly, 0.100 M sodium acetate, 12% glycerol, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.7429.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.144α = 90
b = 57.313β = 90
c = 60.334γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDRh coated flat mirror, toroidal focusing mirror2009-05-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-21.0000SSRLBL9-2

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
11.7925.8997.20.0985.73.51573413690
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.8497.90.37523.32186

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 2H9D1.7925.891529413690153297.340.213570.213570.207930.26403RANDOM20.854
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.415
r_dihedral_angle_4_deg16.521
r_dihedral_angle_3_deg14.738
r_scangle_it5.526
r_dihedral_angle_1_deg5.158
r_scbond_it3.446
r_mcangle_it2.055
r_angle_refined_deg1.874
r_mcbond_it1.238
r_chiral_restr0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.415
r_dihedral_angle_4_deg16.521
r_dihedral_angle_3_deg14.738
r_scangle_it5.526
r_dihedral_angle_1_deg5.158
r_scbond_it3.446
r_mcangle_it2.055
r_angle_refined_deg1.874
r_mcbond_it1.238
r_chiral_restr0.14
r_bond_refined_d0.022
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1519
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms32

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling