4XHF
Crystal structure of Shewanella oneidensis NqrC
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 0.1 M MIB (malonate, imidazole and boric acid), 25% (w/v) PEG 1,500 |
2 | VAPOR DIFFUSION, HANGING DROP | 9 | 293 | 0.1 M bicine, 0.1 M NaCl, 27% (w/v) PEG 1,500, 20% (v/v) ethylene glycol |
Crystal Data
Unit Cell | |
---|---|
Length ( ? ) | Angle ( ? ) |
a = 70.914 | ¦Á = 90 |
b = 93.476 | ¦Â = 100.24 |
c = 71.139 | ¦Ã = 90 |
Symmetry | |
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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 | CCD | ADSC QUANTUM 315r | monochromator | 2014-10-07 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | M | MAD | |||||||||
3 | 2 | |||||||||||||
4 | 2 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97918 | APS | 19-ID |
2 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97918 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.76 | 50 | 99 | 0.065 | 0.075 | 0.036 | 14.4 | 4.1 | 89381 | 89381 |
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 | 1.76 | 1.79 | 96.3 | 0.384 | 0.456 | 0.241 | 0.748 | 3.4 | 4319 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | FREE R-VALUE | 1.76 | 33.713 | 1.37 | 88913 | 2032 | 98.32 | 0.1684 | 0.1657 | 0.2016 | random selection | 23.853 |
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 | 12.031 |
f_angle_d | 0.648 |
f_chiral_restr | 0.026 |
f_bond_d | 0.004 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 6917 |
Nucleic Acid Atoms | |
Solvent Atoms | 651 |
Heterogen Atoms | 197 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-3000 | data reduction |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data scaling |
PHENIX | phasing |