2H0R
Structure of the Yeast Nicotinamidase Pnc1p
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | 298 | 0.9M sodium citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.62 | 78.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 302.04 | α = 90 |
b = 302.04 | β = 90 |
c = 112.12 | 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 | CUSTOM-MADE | 2004-02-11 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | CCD | CUSTOM-MADE | 2004-08-19 | ||||||||||
3 | 1 | CCD | ADSC QUANTUM 210 | 2004-11-23 | ||||||||||
4 | 1 | CCD | ADSC QUANTUM 210 | 2004-11-23 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 1.0332 | APS | 19-BM |
2 | SYNCHROTRON | APS BEAMLINE 19-BM | 1.0719 | APS | 19-BM |
3 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.1401,1.1405,1.1390 | ALS | 8.2.1 |
4 | SYNCHROTRON | ALS BEAMLINE 8.2.1 | 1.8000 | ALS | 8.2.1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.9 | 50 | 100 | 0.07 | 21 | 4.4 | 84498 | 84498 | 71.5 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.9 | 3 | 100 | 0.559 | 3.4 | 4.3 | 8439 |
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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MAD+MIRAS | THROUGHOUT | 2.9 | 50 | 80251 | 80251 | 4226 | 99.95 | 0.19066 | 0.19066 | 0.18912 | 0.21997 | RANDOM | 77.431 |
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] | |
0.7 | 0.35 | 0.7 | -1.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.6 |
r_dihedral_angle_4_deg | 18.218 |
r_dihedral_angle_3_deg | 17.969 |
r_dihedral_angle_1_deg | 6.577 |
r_scangle_it | 2.132 |
r_angle_refined_deg | 1.331 |
r_scbond_it | 1.319 |
r_mcangle_it | 0.778 |
r_mcbond_it | 0.419 |
r_nbtor_refined | 0.312 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12341 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHARP | phasing |