2FWG
high resolution crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (photoreduced form)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2TRX | modified version of 2TRX (see publication) |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 277.15 | 0.1M ammonium acetate, 0.2M sodium acetate, 0.1M sodium iodide, 40% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.61 | 27.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 30.168 | α = 90 |
b = 45.966 | β = 90 |
c = 73.823 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 90.9 | CCD | MARRESEARCH | dynamically bendable mirror | 2003-05-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.8600 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.1 | 16 | 99.7 | 0.124 | 6.9 | 3.9 | 42504 | 42360 | -3 | 11.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.1 | 1.15 | 99.5 | 0.429 | 3 | 5200 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | modified version of 2TRX (see publication) | 1.1 | 16 | 41402 | 41402 | 953 | 0.149 | 0.174 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
17 | 893 | 1118.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_anti_bump_dis_restr | 0.114 |
s_approx_iso_adps | 0.082 |
s_zero_chiral_vol | 0.069 |
s_non_zero_chiral_vol | 0.068 |
s_similar_adp_cmpnt | 0.049 |
s_angle_d | 0.03 |
s_from_restr_planes | 0.0273 |
s_bond_d | 0.02 |
s_rigid_bond_adp_cmpnt | 0.004 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1001 |
Nucleic Acid Atoms | |
Solvent Atoms | 185 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
XDS | data reduction |
XDS | data scaling |
AMoRE | phasing |