4CHE
Crystal structure of the putative cap-binding domain of the PB2 subunit of Thogoto virus polymerase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6 | 293 | THE PROTEIN WAS CONCENTRATED TO 9 MG/ML IN A BUFFER CONTAINING 20 MM TRIS PH 7.0, 200 MM NACL AND 5 MM BETA-MERCAPTOETHANOL. THE BEST-DIFFRACTING CRYSTALS GREW WITHIN 2 DAYS AT 20 C IN A SOLUTION CONTAINING 100 MM BIS-TRIS PH 6.0, 100 MM MGCL2 AND 22 % PEG3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.62 | α = 90 |
b = 109.62 | β = 90 |
c = 39.06 | γ = 90 |
Symmetry | |
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Space Group | I 4 |
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 225 mm CCD | 2008-02-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 |
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 | 1.8 | 50 | 99.7 | 0.06 | 16.5 | 5.2 | 21746 |
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) | |||||||||||
1 | 1.8 | 1.85 | 99.6 | 0.64 | 2.4 | 3.7 |
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 | SAD | THROUGHOUT | NONE | 1.8 | 77.62 | 20631 | 1115 | 99.67 | 0.17268 | 0.17161 | 0.19215 | RANDOM | 25.115 |
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] | |
-0.65 | -0.65 | 1.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.395 |
r_dihedral_angle_4_deg | 16.232 |
r_dihedral_angle_3_deg | 10.836 |
r_dihedral_angle_1_deg | 5.861 |
r_angle_refined_deg | 1.204 |
r_angle_other_deg | 0.803 |
r_chiral_restr | 0.081 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1305 |
Nucleic Acid Atoms | |
Solvent Atoms | 188 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
autoSHARP | phasing |