3REM

Structure of the Isochorismate-Pyruvate Lyase from Pseudomonas aerugionsa with Bound 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 DROP4.52980.2 M lithium sulfate, 0.1 M sodium acetate, 6% glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8934.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.316α = 90
b = 60.254β = 90
c = 60.607γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDRh coated flat mirror, toroidal focusing mirror2010-04-30MSINGLE 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
11.9531.7195.60.05815.43.71301012438
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)
11.952.0697.10.2265.23.41816

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 2H9D1.9531.711243811177123594.60.236650.236650.230860.29084RANDOM16.308
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]
-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.591
r_dihedral_angle_4_deg17.731
r_dihedral_angle_3_deg15.679
r_dihedral_angle_1_deg4.669
r_scangle_it3.094
r_scbond_it1.837
r_angle_refined_deg1.211
r_mcangle_it1.038
r_mcbond_it0.546
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.591
r_dihedral_angle_4_deg17.731
r_dihedral_angle_3_deg15.679
r_dihedral_angle_1_deg4.669
r_scangle_it3.094
r_scbond_it1.837
r_angle_refined_deg1.211
r_mcangle_it1.038
r_mcbond_it0.546
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1564
Nucleic Acid Atoms
Solvent Atoms44
Heterogen Atoms32

Software

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