2H3D
Crystal Structure of Mouse Nicotinamide Phosphoribosyltransferase/Visfatin/Pre-B Cell Colony Enhancing Factor in Complex with Nicotinamide Mononuleotide
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.8 | 291 | 5 mg/ml Se-Met Nampt with 10 mM added NMN and reservoir solution containing 0.1 M HEPES pH 7.8, 0.1 M Na acetate, and 14.5% PEG4000 in a 1:1 ratio in a total initial drop volume of 2 microliter., VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.80 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.46 | α = 90 |
b = 107.96 | β = 96.98 |
c = 83.65 | 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 | 200 | CCD | 2005-07-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | APS | 23-ID-D |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 50 | 98.9 | 0.106 | 13.4 | 3.2 | 61073 | 17.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.1 | 2.18 | 92.6 | 0.332 | 2.7 | 2.4 |
Refinement
Statistics | |||||||||||||||||||
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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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.1 | 40.13 | 61048 | 3043 | 98.6 | 0.215 | 0.215 | 0.238 | RANDOM | 28.4 |
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] | |
8.77 | -7.19 | -3.39 | -5.38 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.4 |
c_scangle_it | 2.98 |
c_scbond_it | 2.08 |
c_mcangle_it | 1.82 |
c_mcbond_it | 1.23 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.77 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7431 |
Nucleic Acid Atoms | |
Solvent Atoms | 163 |
Heterogen Atoms | 44 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
CNS | refinement |
HKL-2000 | data scaling |
CNS | phasing |