3KC6
Crystal structure of the large c-terminal domain of polymerase basic protein 2 from influenza virus a/viet nam/1203/2004 (h5n1)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3CW4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 10.5 | 293 | 5% SBOG, 100MM CAPS PH 10.5, 1.2 M SODIUM PHOSPHATE, 0.2 M LITHIUM PHOSPHATE, 0.8 M POTASSIUM PHOSPHATE. PROTEIN CONCENTRATION 8.25 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.79 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 33.084 | ¦Á = 90 |
b = 65.696 | ¦Â = 90 |
c = 96.855 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | RIGAKU SATURN 944+ | MIRRORS | 2009-08-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.54178 |
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 | 2.05 | 50 | 98.7 | 0.079 | 9.1 | 5.6 | 13728 |
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 | 2.05 | 2.09 | 88.5 | 0.328 | 4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | 3CW4 | 2.05 | 50 | 13682 | 684 | 0.204 | 0.202 | 0.245 | RANDOM | 9.38 |
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] | |
0.29 | -1.01 | 0.72 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.82 |
r_dihedral_angle_4_deg | 20.226 |
r_dihedral_angle_3_deg | 13.746 |
r_dihedral_angle_1_deg | 5.77 |
r_scangle_it | 2.396 |
r_scbond_it | 1.453 |
r_angle_refined_deg | 1.187 |
r_mcangle_it | 1.054 |
r_angle_other_deg | 0.834 |
r_mcbond_it | 0.582 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1503 |
Nucleic Acid Atoms | |
Solvent Atoms | 92 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
StructureStudio | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |