2OFZ
Ultrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N Protein) at 1.1 Angstrom Resolution in Monoclinic Form.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2BTL | structure of homolog from infectious bronchitis virus PDB:2BTL |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 25% PEG 2000MME, 0.2 M sodium bromide, 0.1 M sodium acetate, bcip ADDITIVE, VAPOR DIFFUSION, SITTING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.571 | α = 90 |
b = 36.44 | β = 94.71 |
c = 47.737 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | CCD | MARMOSAIC 325 mm CCD | mirrors | 2005-05-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.9793 | SSRL | BL11-1 |
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 | 1.17 | 47.57 | 97.4 | 0.062 | 0.059 | 22.19 | 3.8 | 40016 | 11.19 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
1.17 | 1.2 | 99.19 | 0.497 | 0.526 | 2.25 | 3.2 | 2882 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | structure of homolog from infectious bronchitis virus PDB:2BTL | 1.17 | 47.57 | 40016 | 40016 | 2131 | 99.78 | 0.1638 | 0.16389 | 0.16244 | 0.19132 | RANDOM | 11.191 |
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] | |
0.16 | 0.05 | 0.3 | -0.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.657 |
r_dihedral_angle_4_deg | 18.229 |
r_dihedral_angle_3_deg | 12.61 |
r_dihedral_angle_1_deg | 5.836 |
r_sphericity_free | 5.087 |
r_scangle_it | 3.208 |
r_sphericity_bonded | 2.95 |
r_scbond_it | 2.286 |
r_mcangle_it | 1.77 |
r_angle_refined_deg | 1.373 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1100 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Blu-Ice | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |