5DSD
The crystal structure of the C-terminal domain of Ebola (Bundibugyo) nucleoprotein
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 4QB0 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | Crystallization solution: 1.33 M LiSO4, 0.1 M Tris pH 8.5. 1:1 ratio (250 nL: 250 nL) of precipitant to protein (at a concentration of 13.9 mg/ml). 60 mcL reservoir. Protein purification buffer 50mM Tris-HCl, 150 mM NaCl; pH 7.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
5.94 | 79 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 108.957 | α = 90 |
b = 108.957 | β = 90 |
c = 82.736 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 64 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX300HE | 2014-08-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.99 | APS | 21-ID-D |
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 | 2.3 | 80 | 94.3 | 0.084 | 20.3 | 14.8 | 12398 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.3 | 2.38 | 64.7 | 0.432 | 0.432 | 1.9 | 7.1 |
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 | 4QB0 | 2.31 | 80 | 11792 | 604 | 94.04 | 0.1692 | 0.1676 | 0.2025 | RANDOM | 81.78 |
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] | |
0.68 | 0.34 | 0.68 | -2.2 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.102 |
r_mcangle_it | 14.363 |
r_mcbond_it | 13.696 |
r_mcbond_other | 13.629 |
r_dihedral_angle_3_deg | 13.36 |
r_dihedral_angle_4_deg | 10.807 |
r_dihedral_angle_1_deg | 5.678 |
r_angle_refined_deg | 1.253 |
r_angle_other_deg | 0.899 |
r_chiral_restr | 0.071 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 861 |
Nucleic Acid Atoms | |
Solvent Atoms | 113 |
Heterogen Atoms | 13 |
Software
Software | |
---|---|
Software Name | Purpose |
PDB_EXTRACT | data extraction |
REFMAC | refinement |
SBC-Collect | data collection |
HKL-3000 | phasing |
SCALEPACK | data scaling |
PHENIX | model building |
HKL-3000 | data reduction |
Coot | model building |