1W54
Stepwise introduction of a zinc binding site into Porphobilinogen synthase from Pseudomonas aeruginosa (mutation D139C)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1B4K | PDB ENTRY 1B4K |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | HANGING DROP IN 24-WELL LIMBRO PLATES. DROPS MADE OF 5 MICROL PROTEIN SOLUTION (8,7 MG/ML PROTEIN, 50 MM NA-HEPES PH 7.5, 10 MM MGCL2, 10 ZNCL2, 10 MM DTT) PLUS 5 MICROL RESERVOIR SOLUTION (28,5 % (W/V) PEG-400, 100 MM NA-HEPES PH 7.5, 80MM MGCL2, 20MM DTT) ABOVE 500 MICROL OF RESERVOIR SOLUTION. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.38 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 125.231 | α = 90 |
b = 125.232 | β = 90 |
c = 86.03 | γ = 90 |
Symmetry | |
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Space Group | P 4 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | RIGAKU R-AXIS IV | BLUE OPTIC | 2002-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 2.2 | 47.1 | 99.8 | 0.1 | 23.1 | 12.6 | 35228 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.28 | 99.5 | 0.45 | 5.3 | 11.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1B4K | 2.2 | 87.71 | 33396 | 1811 | 99.7 | 0.157 | 0.154 | 0.217 | RANDOM | 30.84 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.57 | 0.57 | -1.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 6.203 |
r_dihedral_angle_1_deg | 5.359 |
r_mcangle_it | 4.869 |
r_scbond_it | 4.199 |
r_mcbond_it | 3.553 |
r_angle_refined_deg | 1.928 |
r_angle_other_deg | 1.166 |
r_symmetry_vdw_other | 0.31 |
r_symmetry_vdw_refined | 0.265 |
r_nbd_other | 0.231 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4899 |
Nucleic Acid Atoms | |
Solvent Atoms | 304 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |