3IJR
2.05 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD+
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3I3O | PDB entry 3I3O |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 295 | 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 10mm NAD+. Paratone-N used as a cryoprotectant , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.749 | α = 90 |
b = 123.203 | β = 90 |
c = 169.767 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 300 mm CCD | Beryllium Lenses/Diamond Laue Mono | 2009-07-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
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 | 2.05 | 30 | 100 | 0.071 | 17.19 | 3.9 | 284777 | 284777 | -3 | 29.3 |
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 | 2.05 | 2.09 | 100 | 0.465 | 2.99 | 3.9 | 14257 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3I3O | 2.05 | 30 | 139930 | 139930 | 7373 | 99.59 | 0.15891 | 0.15891 | 0.15709 | 0.19348 | RANDOM | 10.358 |
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] | |
1.42 | 0.71 | -2.14 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.31 |
r_dihedral_angle_4_deg | 12.355 |
r_dihedral_angle_3_deg | 9.923 |
r_scangle_it | 4.146 |
r_dihedral_angle_1_deg | 3.199 |
r_scbond_it | 2.838 |
r_mcangle_it | 1.54 |
r_angle_refined_deg | 1.42 |
r_mcbond_it | 0.966 |
r_angle_other_deg | 0.818 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 17344 |
Nucleic Acid Atoms | |
Solvent Atoms | 932 |
Heterogen Atoms | 430 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |