3V8E
Crystal structure of the yeast nicotinamidase Pnc1p bound to the inhibitor nicotinaldehyde
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | Protein was dialyzed against buffer containing 15 mM Tris pH 7.5, 50 mM NaCl, 4 mM MgCl2, 10 mM Na Citrate and 5 % glycerol and the inhibitor nicotinaldehyde was added at a 4:1 ratio. The protein (5 mg/ml) was mixed with mother liquor (1.6 M NaOAc, 10 % ethylene glycol, 0.1 M HEPES pH 7.4) at a 1:1 (vol) ratio. Crystals were formed by hanging drop vapor diffusion. Crystals were transferred to a cryoprotectant solution (1.5 M NaOAc, 20% ethylene glycol, 0.1M HEPES pH 7.4) and flash-frozen in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 298.717 | α = 90 |
b = 298.717 | β = 90 |
c = 112.652 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | 2009-10-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.7 | 30 | 100 | 5.7 | 101157 | 101147 |
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) | |||||||||||
1 | 2.7 | 2.75 | 100 | 0.348 | 5.3 | 5.5 |
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 | THROUGHOUT | 2.71 | 30 | 96087 | 5058 | 99.71 | 0.18221 | 0.18108 | 0.2031 | RANDOM | 57.356 |
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] | |
0.68 | 0.34 | 0.68 | -1.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.035 |
r_dihedral_angle_3_deg | 17.253 |
r_dihedral_angle_4_deg | 15.903 |
r_dihedral_angle_1_deg | 6.207 |
r_angle_refined_deg | 1.204 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12397 |
Nucleic Acid Atoms | |
Solvent Atoms | 292 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |