4E38
Crystal structure of probable keto-hydroxyglutarate-aldolase from Vibrionales bacterium SWAT-3 (Target EFI-502156)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 294 | 0.1M BIS-TRIS, 0.5M MAGNESIUM FORMATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.503 | α = 90 |
b = 80.96 | β = 90 |
c = 123.6 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | MIRRORS | 2011-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X29A | NSLS | X29A |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.64 | 70 | 98.9 | 0.053 | 10.1 | 8.1 | 92852 | -5 | 28.894 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.64 | 1.67 | 86.8 | 0.094 | 2 | 7.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | MR | THROUGHOUT | PDB entry 1VHC | 1.64 | 67.72 | 89441 | 2765 | 99.3 | 0.17175 | 0.17074 | 0.20438 | RANDOM | 32.187 |
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] | |
-0.56 | 0.49 | 0.07 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.469 |
r_dihedral_angle_4_deg | 17.074 |
r_dihedral_angle_3_deg | 12.633 |
r_scangle_it | 9.864 |
r_scbond_it | 6.571 |
r_dihedral_angle_1_deg | 4.874 |
r_mcangle_it | 4.81 |
r_mcbond_it | 3.243 |
r_angle_refined_deg | 1.318 |
r_chiral_restr | 0.091 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4850 |
Nucleic Acid Atoms | |
Solvent Atoms | 592 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |