3MBC
Crystal structure of monomeric isocitrate dehydrogenase from Corynebacterium glutamicum in complex with NADP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.3 | 298 | 25% polyethylene glycol 2000 monomethyl ether, 0.2 M tris[hydroxymethyl]aminomethane-HCl buffer, 0.2 M MgCl2, and 10 mM NADP, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 128.84 | α = 90 |
b = 52.73 | β = 103.41 |
c = 236.37 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | 2008-03-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.97934 | CLSI | 08ID-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 | 1.9 | 19.74 | 97.8 | 0.088 | 9.94 | 3.66 | 122536 | 119827 | -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 | 1.9 | 1.95 | 85.4 | 0.308 | 3.5 | 3.25 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2b0t split into 2 domains: Domain I (residues 2-138, and 558-737) and Domain II (139-557). | 1.9 | 19.74 | 122536 | 113834 | 5992 | 100 | 0.19137 | 0.18938 | 0.22926 | RANDOM | 30.086 |
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] | |
1.85 | 0.45 | -1.53 | -0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.071 |
r_dihedral_angle_4_deg | 14.947 |
r_dihedral_angle_3_deg | 13.795 |
r_dihedral_angle_1_deg | 6.139 |
r_scangle_it | 3.947 |
r_mcangle_it | 2.864 |
r_scbond_it | 2.819 |
r_mcbond_it | 2.163 |
r_angle_refined_deg | 1.272 |
r_angle_other_deg | 0.824 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11204 |
Nucleic Acid Atoms | |
Solvent Atoms | 796 |
Heterogen Atoms | 33 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Macromolecular | data collection |
XDS | data reduction |