2C14

5-(4-Carboxy-2-oxo-butylamino)-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, 50 MM TRIS-HCL, PH 7.5, 5 MM MGCL2, 1MM NACL, 1 MM 5-(4-CARBOXY-2-OXO-BUTYLAMINO)-4-OXO-PENTANOIC ACID MONOSODIUM SALT)) PLUS 5 MICROL RESERVOIR SOLUTION (18.0 % (W/V) PEG-3350, 200 MM LINO3)
Crystal Properties
Matthews coefficientSolvent content
2.346.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.877α = 90
b = 126.877β = 90
c = 86.098γ = 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
11.940.1398.80.169.97.855853
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)
11.91.9495.20.4827

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 1B4K1.989.852367280298.80.160.1580.201RANDOM18.02
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]
0.460.46-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.899
r_dihedral_angle_4_deg18.464
r_dihedral_angle_3_deg14.812
r_dihedral_angle_1_deg5.917
r_scangle_it3.128
r_scbond_it2.115
r_angle_refined_deg1.525
r_mcangle_it1.207
r_mcbond_it0.788
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.899
r_dihedral_angle_4_deg18.464
r_dihedral_angle_3_deg14.812
r_dihedral_angle_1_deg5.917
r_scangle_it3.128
r_scbond_it2.115
r_angle_refined_deg1.525
r_mcangle_it1.207
r_mcbond_it0.788
r_nbtor_refined0.295
r_nbd_refined0.231
r_symmetry_vdw_refined0.203
r_symmetry_hbond_refined0.162
r_xyhbond_nbd_refined0.143
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.007
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 Atoms5149
Nucleic Acid Atoms
Solvent Atoms723
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling