1W5M | pdb_00001w5m

Stepwise introduction of zinc binding site into porphobilinogen synthase of Pseudomonas aeruginosa (mutations A129C 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 DROP8.5HANGING DROP. DROPS WERE MIXED OF 5 MICROLITER OF PROTEIN SOLUTION (7.5 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 8.5, 200 MM MGCL2, 20MM BETA-MERCAPTOETHANOLE) ON GLASS COVER SLIDES, HANGING ABOVE 500 MICROLITER OF RESERVOIR SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.2444.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.307α = 90
b = 126.307β = 90
c = 85.156γ = 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
11.62099.90.0532.76.490595
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)
11.61.631000.285.56.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1B4K1.687.71855494488990.1310.1290.140.1650.18RANDOM14.2
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]
0.240.24-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.214
r_dihedral_angle_4_deg17.121
r_dihedral_angle_3_deg13.493
r_scangle_it6.727
r_dihedral_angle_1_deg5.767
r_scbond_it4.679
r_mcangle_it3.479
r_mcbond_it2.744
r_angle_refined_deg2.061
r_angle_other_deg1.034
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.214
r_dihedral_angle_4_deg17.121
r_dihedral_angle_3_deg13.493
r_scangle_it6.727
r_dihedral_angle_1_deg5.767
r_scbond_it4.679
r_mcangle_it3.479
r_mcbond_it2.744
r_angle_refined_deg2.061
r_angle_other_deg1.034
r_symmetry_vdw_other0.278
r_nbd_refined0.233
r_nbd_other0.202
r_nbtor_refined0.182
r_symmetry_vdw_refined0.176
r_chiral_restr0.157
r_symmetry_hbond_refined0.121
r_xyhbond_nbd_refined0.12
r_nbtor_other0.086
r_bond_refined_d0.023
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms5051
Nucleic Acid Atoms
Solvent Atoms887
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing