4HNO
High resolution crystal structure of DNA Apurinic/apyrimidinic (AP) endonuclease IV Nfo from Thermatoga maritima
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QTW | PDB ENTRY 1QTW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 298 | 100 mM Tris-HCl pH 9.0, 4 mM DTT, 1.5% saturated MgSO4, 16% ethylene glycol, 20% mPEG2K, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 123.37 | α = 90 |
b = 123.37 | β = 90 |
c = 35.395 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 90 | IMAGE PLATE | MAR scanner 345 mm plate | 1999-07-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL9-1 | 0.78 | SSRL | BL9-1 |
Data Collection
Overall | |||||||||||||||||||
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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 | 0.9194 | 30 | 95.9 | 0.053 | 10.8 | 2.84 | 213629 | 204938 | 5 | 5 | 26.5 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
1 | 0.9194 | 0.95 | 88.6 | 0.42 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 1QTW | 0.9194 | 24.511 | 1.34 | 204931 | 204917 | 10253 | 95.92 | 0.1255 | 0.1248 | 0.139 | 17.0195 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.775 |
f_angle_d | 1.311 |
f_chiral_restr | 0.08 |
f_bond_d | 0.017 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2267 |
Nucleic Acid Atoms | |
Solvent Atoms | 427 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
EPMR | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |