3F1K
Crystal Structure of yciK from E. coli, an oxidoreductase, complexed with NADP+ at 2.6A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.6 | 295 | 0.1M Sodium Acetate monohydrate pH 4.6, 8% w/v polyethylene glycol 4000, vapor diffusion, hanging drop, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.21 | 61.67 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.509 | α = 90 |
b = 88.509 | β = 90 |
c = 80.419 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MAR CCD 300 mm | Si(III) Monochromator | 2007-11-01 | M | MAD | |||||
2 | 1 | x-ray | 100 | CCD | MAR CCD 165 mm | Diamond (III) Monochromator | 2007-11-23 | M | SAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.97887, 0.97864, 0.96860 | APS | 21-ID-D |
2 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97990 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.5 | 44.25 | 99.9 | 0.114 | 16.6 | 21.76 | 12975 | 53.3 |
Highest Resolution Shell | |||||||||||||||||||
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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) | |||||||||||
2.5 | 2.59 | 100 | 0.424 | 6.3 | 21.4 | 1282 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||||
X-RAY DIFFRACTION | MAD, SAD | 2.6 | 35.608 | 21570 | 2188 | 99.62 | 0.216 | 0.211 | 0.261 | 58.194 |
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] | |
-3.711 | -3.711 | 7.423 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.705 |
f_angle_d | 1.416 |
f_chiral_restr | 0.082 |
f_bond_d | 0.01 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1956 |
Nucleic Acid Atoms | |
Solvent Atoms | 49 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data processing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
d*TREK | data reduction |
d*TREK | data scaling |
PHENIX | phasing |