2C13

5-hydroxy-levulinic acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7HANGING DROP IN 24-WELL LIMBRO PLATES.DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.05 M TRIS-HCL, PH 7.5, 0.005 M MGCL2, 0.01 M 5-OH-4-OXO-PENTANOIC ACID SODIUM SALT PLUS 5 MICROL RESERVOIR SOLUTION 9.0 % (W/V) PEG-4000, 0.180 M KCL, 0.009 M CACL2, 0.05 M NA-CACODYLATE PH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.345.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.314α = 90
b = 126.314β = 90
c = 85.481γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU-MSC R-AXIS IVBLUE OPTIC2005-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
12.1540.299.50.1316.7113788122.5
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)
12.152.2399.20.464.99.9

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 1B4K2.1589.837848193199.20.1550.1520.204RANDOM17.69
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]
-0.047-0.0470.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.609
r_dihedral_angle_4_deg20.346
r_dihedral_angle_3_deg15.736
r_dihedral_angle_1_deg9.615
r_scangle_it3.586
r_scbond_it2.407
r_angle_refined_deg1.696
r_mcangle_it1.262
r_mcbond_it0.725
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.609
r_dihedral_angle_4_deg20.346
r_dihedral_angle_3_deg15.736
r_dihedral_angle_1_deg9.615
r_scangle_it3.586
r_scbond_it2.407
r_angle_refined_deg1.696
r_mcangle_it1.262
r_mcbond_it0.725
r_nbtor_refined0.302
r_symmetry_vdw_refined0.235
r_nbd_refined0.226
r_symmetry_hbond_refined0.165
r_xyhbond_nbd_refined0.136
r_chiral_restr0.13
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5161
Nucleic Acid Atoms
Solvent Atoms457
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling