1VLC
Crystal structure of 3-isopropylmalate dehydrogenase (TM0556) from Thermotoga maritima at 1.90 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 9 | 277 | 25.0% PEG-4000, 0.2M Li2SO4, 0.1M TRIS pH 9.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
2 | VAPOR DIFFUSION,SITTING DROP,NANODROP | 7.5 | 277 | 20.0% PEG-8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.84 | 56.62 |
2.91 | 57.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 118.78 | α = 90 |
b = 118.78 | β = 90 |
c = 56.699 | γ = 120 |
Symmetry | |
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Space Group | P 3 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 | ADSC QUANTUM 315 | flat mirror | 2004-06-27 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | M | MAD | |||||||||
1,2 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | SSRL | BL11-1 | |
2 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.979251, 0.979508, 0.885567 | SSRL | BL11-1 |
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 | ||||||||
1,2 | 1.9 | 41.01 | 99.5 | 0.11 | 13.6 | 5.6 | 36394 | 39.46 |
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) | |||||||||||
1,2 | 1.9 | 1.95 | 97.2 | 0.684 | 1.9 | 3.6 | 2598 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.9 | 41.01 | 34079 | 1801 | 98.15 | 0.18934 | 0.18779 | 0.21822 | RANDOM | 30.46 |
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] | |
1.45 | 0.73 | 1.45 | -2.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.297 |
r_dihedral_angle_4_deg | 19.243 |
r_dihedral_angle_3_deg | 13.779 |
r_scangle_it | 8.908 |
r_scbond_it | 6.495 |
r_dihedral_angle_1_deg | 6.197 |
r_mcangle_it | 3.795 |
r_mcbond_it | 2.902 |
r_angle_refined_deg | 1.673 |
r_angle_other_deg | 0.872 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2723 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | model building |
autoSHARP | phasing |
SOLOMON | phasing |
REFMAC | refinement |
CCP4 | data scaling |
SHELX | phasing |