4D5T
Structure of N-terminally truncated A49 from Vaccinia Virus Western Reserve
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4D5R | PDB ENTRY 4D5R |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 293 | PROTEIN (1 UL AT 25.0 MG/ML) WAS MIXED WITH 1 UL RESERVOIR SOLUTION AND EQUILIBRATED AT 20 C AGAINST 500 UL RESERVOIRS CONTAINING 0.1 M HEPES PH 7.5, 1.6 M AMMONIUM SULFATE AND 1.5% (VOL/VOL) PEG 400. CRYSTALS WERE CRYOPROTECTED BY PASSAGE THROUGH 2 UL OF PERFLUOROPOLYETHER OIL (HAMPTON RESEARCH) THAT HAD BEEN OVERLAID ONTO THE MOTHER LIQUOR. |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.26 | 45.6 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 92.29 | α = 90 |
b = 45.63 | β = 98.74 |
c = 160.26 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2013-03-02 | 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 | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.84 | 45.7 | 97.9 | 0.07 | 13.6 | 6.8 | 112855 | -3 | 21.6 |
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 | 1.84 | 1.89 | 96 | 1.16 | 1.5 | 6.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PDB ENTRY 4D5R | 1.84 | 45.71 | 107126 | 5665 | 97.61 | 0.20801 | 0.20638 | 0.23888 | RANDOM | 36.864 |
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] | |
-2.12 | 0.82 | 0.49 | 1.31 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.482 |
r_dihedral_angle_4_deg | 16.898 |
r_dihedral_angle_3_deg | 13.285 |
r_dihedral_angle_1_deg | 5.509 |
r_scbond_it | 2.998 |
r_mcangle_it | 2.868 |
r_mcbond_it | 2.06 |
r_mcbond_other | 2.06 |
r_angle_other_deg | 1.988 |
r_angle_refined_deg | 1.689 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 9714 |
Nucleic Acid Atoms | |
Solvent Atoms | 894 |
Heterogen Atoms | 25 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |