3C2V
Crystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP and the inhibitor phthalate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | 20% PEG 3350, 0.2 M ammonium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 50.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 154.668 | α = 90 |
b = 154.668 | β = 90 |
c = 69.346 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 110 | CCD | BRUKER SMART 2000 | 2005-12-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR-H | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.3 | 50 | 99.2 | 0.083 | 0.083 | 3.95 | 4.6 | 14205 | 14089 | 1 | 1 | 50.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2.3 | 2.38 | 98.4 | 0.39 | 0.39 | 3.95 | 4 | 1388 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 2.29 | 44.63 | 12818 | 514 | 90.99 | 0.227 | 0.225 | 0.282 | RANDOM | 50.579 |
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] | |
-5.24 | -2.62 | -5.24 | 7.86 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.358 |
r_dihedral_angle_4_deg | 19.919 |
r_dihedral_angle_3_deg | 15.1 |
r_dihedral_angle_1_deg | 12.026 |
r_scangle_it | 3.093 |
r_scbond_it | 2.131 |
r_mcangle_it | 1.704 |
r_angle_refined_deg | 1.675 |
r_mcbond_it | 0.983 |
r_chiral_restr | 0.578 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2067 |
Nucleic Acid Atoms | |
Solvent Atoms | 149 |
Heterogen Atoms | 34 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PROTEUM PLUS | data collection |
SAINT | data reduction |