4D5R
Structure of N-terminally truncated A49 from Vaccinia Virus Western Reserve
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 293 | CRYSTALS WERE GROWN BY MIXING 2 UL PROTEIN (20-21 MG/ML) WITH 2 UL RESERVOIR SOLUTION AND EQUILIBRATING AT 20 C AGAINST 500 UL RESERVOIRS CONTAINING 1.3- 1.5 M SODIUM MALONATE PH 6.8, 1% (VOL/VOL) PEG 400 AND 4-10% (VOL/VOL) GLYCEROL, THE BEST CRYSTALS BEING OBTAINED WHEN THE RESERVOIR WAS OVERLAID WITH 100 UL OF A 1:1 MIXTURE OF PARAFFIN AND SILICONE OIL (MOLECULAR DIMENSIONS). CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION IN 2.1 M SODIUM MALONATE, 1% (VOL/VOL) PEG 400 AND 5% (VOL/VOL) GLYCEROL. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.85 | α = 90 |
b = 42.74 | β = 100.51 |
c = 67.19 | 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 | PIXEL | DECTRIS PILATUS 2M | TOROIDAL MIRRORS | 2013-05-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | Diamond | I04-1 |
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 | 1.9 | 33 | 99.6 | 0.04 | 32.2 | 14.1 | 25211 | -3 | 38.3 |
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) | |||||||||||
1 | 1.9 | 1.95 | 99 | 1.15 | 2.9 | 13.5 |
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 | SIRAS | THROUGHOUT | NONE | 1.9 | 33.03 | 23928 | 1279 | 99.51 | 0.18735 | 0.18521 | 0.2264 | RANDOM | 61.597 |
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] | |
-1.85 | -0.3 | 5.38 | -3.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.967 |
r_dihedral_angle_4_deg | 21.013 |
r_dihedral_angle_3_deg | 13.086 |
r_dihedral_angle_1_deg | 5.672 |
r_mcangle_it | 4.527 |
r_scbond_it | 4.518 |
r_mcbond_it | 3.548 |
r_mcbond_other | 3.545 |
r_angle_refined_deg | 1.749 |
r_angle_other_deg | 1.239 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2399 |
Nucleic Acid Atoms | |
Solvent Atoms | 85 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
autoSHARP | phasing |