2PH1
Crystal structure of nucleotide-binding protein AF2382 from Archaeoglobus fulgidus, Northeast Structural Genomics Target GR165
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH UNDER OIL | 7.5 | 293 | Protein solution: 20 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Precipitant solution: 100 mM HEPES pH 7.5, 55% MPD, MICROBATCH UNDER OIL, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.937 | α = 90 |
b = 78.186 | β = 90 |
c = 49.597 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | ADSC QUANTUM 4 | mirrors | 2007-03-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X4A | 0.97950 | NSLS | X4A |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.7 | 49.6 | 100 | 0.086 | 0.079 | 18.54 | 5 | 13903 | 13903 | 35.1 |
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) | ||||||||||
1 | 2.7 | 2.8 | 100 | 0.413 | 0.344 | 5.08 | 5 | 1539 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | THROUGHOUT | 2.7 | 49.6 | 2 | 13903 | 12442 | 1211 | 90.1 | 0.218 | 0.217 | 0.217 | 0.278 | RANDOM | 39 |
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] | |
-15.84 | 14.77 | 1.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 23.2 |
c_angle_deg | 1.2 |
c_improper_angle_d | 0.95 |
c_bond_d | 0.008 |
c_bond_d_na | |
c_bond_d_prot | |
c_angle_d | |
c_angle_d_na | |
c_angle_d_prot | |
c_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1898 |
Nucleic Acid Atoms | |
Solvent Atoms | 37 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
ADSC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SnB | phasing |
RESOLVE | phasing |