1W5O

Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C, 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, SITTING DROP6SITTING DROP. DROPS WERE MIXED OF 3 MICROLITER OF PROTEIN SOLUTION (7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10MM MGCL2, 10MM ZNCL2, 10 MM DTT) PLUS 3 MICROLITER OF RESERVOIR SOLUTION (1M K/NA-TARTRATE, 100MM MES PH 6.0, 20MM BETA-MERCAPTOETHANOLE), 100 MICROLITER OF RESERVOIR SOLUTION, 96 WELL PLATES (NUNC)
Crystal Properties
Matthews coefficientSolvent content
2.2745.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.991α = 90
b = 126.991β = 90
c = 85.369γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2002-02-18MSINGLE 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
11.852099.90.129.614.359936
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)
11.851.881000.319.314.6

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 1B4K1.8591.2956718301299.60.1340.1310.176RANDOM20.09
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]
0.30.3-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.728
r_dihedral_angle_1_deg6.022
r_scbond_it4.646
r_mcangle_it4.053
r_mcbond_it3.012
r_angle_refined_deg2.01
r_angle_other_deg0.987
r_symmetry_vdw_refined0.407
r_symmetry_vdw_other0.342
r_nbd_other0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.728
r_dihedral_angle_1_deg6.022
r_scbond_it4.646
r_mcangle_it4.053
r_mcbond_it3.012
r_angle_refined_deg2.01
r_angle_other_deg0.987
r_symmetry_vdw_refined0.407
r_symmetry_vdw_other0.342
r_nbd_other0.26
r_nbd_refined0.234
r_symmetry_hbond_refined0.162
r_chiral_restr0.153
r_xyhbond_nbd_refined0.135
r_nbtor_other0.09
r_bond_refined_d0.025
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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 Atoms5042
Nucleic Acid Atoms
Solvent Atoms654
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing