1W5N

Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations D131C and D139C)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B4KPDB ENTRY 1B4K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (9 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM BETA-MERCAPTOETHANOLE) PLUS 5 MICROLITER OF RESERVOIR SOLUTION (30.0 % (W/V) PEG 400, 100MM NA-HEPES PH 7.5, 40 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES, HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.2244.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.322α = 90
b = 125.322β = 90
c = 85.795γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2002-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW6MPG/DESY, HAMBURGBW6

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
11.652099.40.0520.55.481768
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)
11.651.71990.363.15.1

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 1B4K1.6587.7176946403098.40.1520.1510.188RANDOM19.9
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]
0.280.28-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.372
r_dihedral_angle_4_deg18.683
r_dihedral_angle_3_deg13.599
r_scangle_it7.787
r_dihedral_angle_1_deg5.535
r_scbond_it5.407
r_mcangle_it4.68
r_mcbond_it3.521
r_angle_refined_deg2.105
r_angle_other_deg1.146
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.372
r_dihedral_angle_4_deg18.683
r_dihedral_angle_3_deg13.599
r_scangle_it7.787
r_dihedral_angle_1_deg5.535
r_scbond_it5.407
r_mcangle_it4.68
r_mcbond_it3.521
r_angle_refined_deg2.105
r_angle_other_deg1.146
r_symmetry_vdw_refined0.302
r_symmetry_vdw_other0.293
r_nbd_refined0.239
r_nbd_other0.189
r_nbtor_refined0.181
r_symmetry_hbond_refined0.175
r_chiral_restr0.165
r_xyhbond_nbd_refined0.148
r_nbtor_other0.086
r_bond_refined_d0.026
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms5001
Nucleic Acid Atoms
Solvent Atoms626
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing