4YOK
Crystal structure of a DUF3823 family protein (PARMER_04126) from Parabacteroides merdae ATCC 43184 at 1.80 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.33 | 293 | 0.2M magnesium chloride, 32.0% polyethylene glycol 1000, 0.01M GSH (L-Glutathione reduced), GSSG (L-Glutathione oxidized), 0.1M sodium cacodylate pH 6.33 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.11 | 41.77 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 41.866 | α = 90 |
b = 66.212 | β = 90 |
c = 68.593 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 21 |
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 | MARMOSAIC 325 mm CCD | Vertical focusing mirror; double crystal Si(111) monochromator | 2014-12-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL14-1 | 0.97947 | SSRL | BL14-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.8 | 26.531 | 99 | 0.062 | 0.078 | 11.04 | 2.58 | 18276 | -3 | 22.698 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.8 | 1.86 | 98.3 | 0.649 | 0.821 | 1.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.8 | 26.531 | 18214 | 925 | 99.78 | 0.1753 | 0.1733 | 0.2141 | RANDOM | 29.4735 |
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] | |
-0.0591 | -4.7125 | 4.7716 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_omega_torsion | 4.08 |
t_other_torsion | 2.54 |
t_angle_deg | 1.05 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1514 |
Nucleic Acid Atoms | |
Solvent Atoms | 174 |
Heterogen Atoms | 9 |
Software
Software | |
---|---|
Software Name | Purpose |
PDB_EXTRACT | data extraction |
SHELX | phasing |
SHARP | phasing |
XDS | data scaling |
XSCALE | data scaling |
BUSTER-TNT | refinement |
SHELXD | phasing |
BUSTER | refinement |
XDS | data reduction |