5NA8
Structure of DPP III from Bacteroides thetaiotaomicron in closed form
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.2 M NaCl, 0.1 M sodium cocodylate pH 6.5, 2.0 M NH4SO4 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.62 | 53.04 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 123.632 | α = 90 |
b = 176.315 | β = 90 |
c = 74.177 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 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 | PIXEL | DECTRIS PILATUS 2M | 2015-05-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 5.2R | 0.97600 | ELETTRA | 5.2R |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 3.27 | 47.49 | 97.5 | 0.229 | 0.254 | 0.109 | 0.974 | 7.8 | 5.3 | 25217 | 47.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 3.27 | 3.49 | 87.1 | 0.592 | 0.669 | 0.305 | 0.831 | 4.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 5NA6 | 3.29 | 47.488 | 1.34 | 25121 | 1241 | 99.04 | 0.2093 | 0.2072 | 0.2506 | 41.0014 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 11.386 |
f_angle_d | 0.416 |
f_chiral_restr | 0.039 |
f_plane_restr | 0.003 |
f_bond_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 10198 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 22 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |