2PN3
Crystal Structure of Hepatitis C Virus IRES Subdomain IIa
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 6.2 | 290 | 5% MPD, 5mM MgSO4, 12.5mM NaCl, 50mM KCl, 25mM Cacodylate equilibrated with 65%MPD, pH 6.2, EVAPORATION, temperature 290.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.55 | 51.74 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.945 | α = 90 |
b = 48.945 | β = 90 |
c = 120.942 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | 77 | CCD | MAR CCD 165 mm | mirrors | 2004-10-30 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 0.9203, 0.9197, 0.90686 | APS | 14-ID-B |
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 | 2.9 | 50 | 93.7 | 0.081 | 27.5 | 11.2 | 3650 | 3420 | 55.3 |
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) | |||||||||||
2.9 | 3 | 75.1 | 0.345 | 4.6 | 8.1 | 253 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.9 | 45 | 3452 | 3202 | 143 | 92.74 | 0.23204 | 0.22969 | 0.2288 | 0.28263 | RANDOM | 44.297 |
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] | |
-2.08 | -2.08 | 4.16 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_scangle_it | 2.006 |
r_angle_refined_deg | 1.885 |
r_scbond_it | 1.177 |
r_symmetry_hbond_refined | 0.305 |
r_nbtor_refined | 0.299 |
r_nbd_refined | 0.195 |
r_xyhbond_nbd_refined | 0.193 |
r_symmetry_vdw_refined | 0.172 |
r_chiral_restr | 0.071 |
r_bond_refined_d | 0.012 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | |
Nucleic Acid Atoms | 930 |
Solvent Atoms | |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
APS | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SOLVE | phasing |