2J5S
Structural of ABDH, a beta-diketone hydrolase from the Cyanobacterium Anabaena sp. PCC 7120 bound to (S)-3-oxocyclohexyl acetic acid
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 0.1 M BIS-TRIS PROPANE PH 7.5, 20% PEG 3350, 0.2 M SODIUM MALONATE, 0.01 M BICYCLO[2.2.2]OCTANE-2,6-DIONE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.61 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.387 | α = 90 |
b = 80.387 | β = 90 |
c = 125.882 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | CCD | ADSC CCD | TOROIDAL MIRROR | 2006-05-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
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 | 1.57 | 40.19 | 98.9 | 0.06 | 32.04 | 10.1 | 64435 |
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 | 1.57 | 1.63 | 89.9 | 0.27 | 2.93 | 4.8 |
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 1O8U | 1.57 | 40.19 | 60411 | 3228 | 98.8 | 0.14 | 0.138 | 0.17 | RANDOM | 14.19 |
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] | |
0.49 | 0.25 | 0.49 | -0.74 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.768 |
r_dihedral_angle_4_deg | 14.64 |
r_dihedral_angle_3_deg | 11.806 |
r_dihedral_angle_1_deg | 5.986 |
r_scangle_it | 2.542 |
r_scbond_it | 1.755 |
r_angle_refined_deg | 1.518 |
r_mcangle_it | 1.146 |
r_mcbond_it | 0.792 |
r_nbtor_refined | 0.317 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4016 |
Nucleic Acid Atoms | |
Solvent Atoms | 490 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |