2C15

5-(4-Carboxy-2-oxo-butoxy)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 100 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 5 MM 5-(4-CARBOXY-2-OXO-BUTOXY)-4-OXO-PENTANOIC ACID SODIUM SALT) PLUS 5 MICROL RESERVOIR SOLUTION (12.0 % (W/V) PEG-8000, 340 MM LI2SO4, 20% (V/V) GLYCEROL,)ABOVE 500 MICROL OF RESERVOIR SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.347

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.538α = 90
b = 127.538β = 90
c = 85.79γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2005-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.4838.196.20.0819.36.8117544
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)
11.481.5198.20.363.16.1

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 1B4K1.4890.17107399565396.20.1490.1480.171RANDOM11.31
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]
0.050.05-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.107
r_dihedral_angle_4_deg16.561
r_dihedral_angle_3_deg12.814
r_dihedral_angle_1_deg5.4
r_scangle_it2.232
r_scbond_it1.486
r_angle_refined_deg1.249
r_mcangle_it0.863
r_mcbond_it0.548
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.107
r_dihedral_angle_4_deg16.561
r_dihedral_angle_3_deg12.814
r_dihedral_angle_1_deg5.4
r_scangle_it2.232
r_scbond_it1.486
r_angle_refined_deg1.249
r_mcangle_it0.863
r_mcbond_it0.548
r_nbtor_refined0.303
r_nbd_refined0.236
r_symmetry_vdw_refined0.173
r_symmetry_hbond_refined0.108
r_xyhbond_nbd_refined0.095
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.005
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 Atoms5146
Nucleic Acid Atoms
Solvent Atoms969
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling