2C13
5-hydroxy-levulinic acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | HANGING DROP IN 24-WELL LIMBRO PLATES.DROPS MADE OF 5 MICROL PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.05 M TRIS-HCL, PH 7.5, 0.005 M MGCL2, 0.01 M 5-OH-4-OXO-PENTANOIC ACID SODIUM SALT PLUS 5 MICROL RESERVOIR SOLUTION 9.0 % (W/V) PEG-4000, 0.180 M KCL, 0.009 M CACL2, 0.05 M NA-CACODYLATE PH 6.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 45.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.314 | α = 90 |
b = 126.314 | β = 90 |
c = 85.481 | 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-MSC R-AXIS IV | BLUE OPTIC | 2005-01-31 | 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 | 2.15 | 40.2 | 99.5 | 0.13 | 16.7 | 11 | 37881 | 22.5 |
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 | 2.15 | 2.23 | 99.2 | 0.46 | 4.9 | 9.9 |
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 | 2.15 | 89.8 | 37848 | 1931 | 99.2 | 0.155 | 0.152 | 0.204 | RANDOM | 17.69 |
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] | |
-0.047 | -0.047 | 0.095 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.609 |
r_dihedral_angle_4_deg | 20.346 |
r_dihedral_angle_3_deg | 15.736 |
r_dihedral_angle_1_deg | 9.615 |
r_scangle_it | 3.586 |
r_scbond_it | 2.407 |
r_angle_refined_deg | 1.696 |
r_mcangle_it | 1.262 |
r_mcbond_it | 0.725 |
r_nbtor_refined | 0.302 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5161 |
Nucleic Acid Atoms | |
Solvent Atoms | 457 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |