1F8G
THE X-RAY STRUCTURE OF NICOTINAMIDE NUCLEOTIDE TRANSHYDROGENASE FROM RHODOSPIRILLUM RUBRUM COMPLEXED WITH NAD+
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 290 | 10mM NAD (+), 25% methylethyl PEG 2000, 200mM sodium phosphate buffer, pH7.5, 30mM Ammonium sulphate. , VAPOR DIFFUSION, HANGING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 46.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.9 | α = 90 |
b = 116.6 | β = 104.22 |
c = 102 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | IMAGE PLATE | MARRESEARCH | 1999-10-30 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | 100 | IMAGE PLATE | MARRESEARCH | 1999-10-30 | |||||||||
3 | 1 | 100 | IMAGE PLATE | MARRESEARCH | 1999-10-30 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | ESRF | BM30A | |
2 | SYNCHROTRON | ESRF BEAMLINE BM30A | ESRF | BM30A | |
3 | SYNCHROTRON | ESRF BEAMLINE BM30A | ESRF | BM30A |
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 | 20 | 94.7 | 0.043 | 14.1 | 3.22 | 99140 | 99140 | 23.3 |
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) | |||||||||||
2 | 2.05 | 89.4 | 0.271 | 2.6 | 5966 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MAD | THROUGHOUT | 2 | 20 | 90649 | 90649 | 4776 | 0.21 | 0.26 | 5% random |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_angle_d | 0.025 |
p_bond_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11116 |
Nucleic Acid Atoms | |
Solvent Atoms | 1459 |
Heterogen Atoms | 158 |
Software
Software | |
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Software Name | Purpose |
MLPHARE | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |