2PGN
The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-dione Hydrolase in Complex with Cyclohexane-1,2-dione
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | 23% PEG 400, 0.01M sodium acetate, 3mM HEPES, 0.5mM ThDP, 0.5mM NAD, 0.1M NaCl. Crystal soaked in 47% PEG 400, 0.02M sodium acetate, 5mM 1,2 cyclohexanedione, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 123.6 | α = 90 |
b = 123.6 | β = 90 |
c = 144.3 | γ = 90 |
Symmetry | |
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Space Group | P 41 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 | CCD | MARMOSAIC 225 mm CCD | 2005-03-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.00 | SLS | X10SA |
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 | 1.1 | 40 | 84.8 | 0.068 | 13.58 | 6.1 | 388867 | 379045 | 12.26 |
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 | 1.1 | 1.2 | 49.9 | 0.487 | 2.7 | 3.6 | 50802 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | known crystal structure | THROUGHOUT | 1.2 | 10 | 333858 | 333858 | 16593 | 97.17 | 0.15 | 0.15 | 0.149 | 0.176 | RANDOM | 12.78 |
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] | |
0.75 | 0.75 | -1.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.859 |
r_dihedral_angle_4_deg | 16.822 |
r_dihedral_angle_3_deg | 13.719 |
r_sphericity_free | 8.377 |
r_dihedral_angle_1_deg | 6.736 |
r_sphericity_bonded | 5.477 |
r_scangle_it | 4.005 |
r_scbond_it | 3.235 |
r_mcangle_it | 2.394 |
r_rigid_bond_restr | 2.139 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8886 |
Nucleic Acid Atoms | |
Solvent Atoms | 1268 |
Heterogen Atoms | 290 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
XDS | data reduction |