3HGW
Apo Structure of Pseudomonas aeruginosa Isochorismate-Pyruvate Lyase I87T mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2H9D | PDB ENTRY 2H9D |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 298.15 | 0.1M Bis-tris propane, pH 6.5, 0.14 M calcium chloride, 23% PEG 3350, and 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.01 | 38.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.503 | α = 90 |
b = 74.919 | β = 90 |
c = 88.505 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 113.15 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2006-07-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 1.54 |
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 | 2.25 | 100 | 99.3 | 0.1 | 14.686 | 7 | 17729 |
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) | |||||||||||
2.25 | 2.33 | 98.5 | 0.354 | 7 | 1726 |
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 2H9D | 2.25 | 23.21 | 17678 | 900 | 99.31 | 0.221 | 0.219 | 0.256 | RANDOM | 20.028 |
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] | |
0.01 | 0.03 | -0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.775 |
r_dihedral_angle_4_deg | 14.815 |
r_dihedral_angle_3_deg | 14.049 |
r_dihedral_angle_1_deg | 4.682 |
r_scangle_it | 2.137 |
r_scbond_it | 1.296 |
r_angle_refined_deg | 1.023 |
r_mcangle_it | 0.824 |
r_mcbond_it | 0.555 |
r_nbtor_refined | 0.292 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2722 |
Nucleic Acid Atoms | |
Solvent Atoms | 76 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |