3GNN
Crystal structure of nicotinate-nucleotide pyrophosphorylase from Burkholderi pseudomallei
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 289 | HAMPTON CRYSTAL SCREEN CONDITION E8, 1.5 M NACL, 10% ETHANOL WITH 25% GLYCEROL AS CRYO-PROTECTANT, 28.7 MG/ML PROTEIN, CRYSTAL ID 109334E8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 160.978 | α = 90 |
b = 57.414 | β = 106.74 |
c = 66.243 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | 2008-06-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-D | 0.97934 | APS | 23-ID-D |
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 | 2.25 | 50 | 98.9 | 0.068 | 21.998 | 3.8 | 27262 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
2.25 | 2.33 | 97.7 | 0.589 | 2.27 | 3.7 | 2650 |
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 | 2.25 | 39.14 | 27260 | 1366 | 98.67 | 0.217 | 0.214 | 0.273 | RANDOM | 48.358 |
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] | |
1.08 | 2.07 | -2.44 | 2.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.522 |
r_dihedral_angle_4_deg | 19.676 |
r_dihedral_angle_3_deg | 19.167 |
r_dihedral_angle_1_deg | 6.585 |
r_scangle_it | 4.725 |
r_scbond_it | 2.895 |
r_mcangle_it | 2.016 |
r_angle_refined_deg | 1.791 |
r_mcbond_it | 1.101 |
r_angle_other_deg | 1.074 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3776 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |