2FWH
atomic resolution crystal structure of the C-terminal domain of the electron transfer catalyst DsbD (reduced form at pH7)
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 |
1.7 | 28.110168 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 30.289 | α = 90 |
b = 46.072 | β = 90 |
c = 74.07 | 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 | 101 | CCD | MARRESEARCH | dynamically bendable mirror | 2004-06-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.8555 | 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 | 0.99 | 20 | 99.6 | 0.079 | 18.8 | 5.8 | 58388 | -3 | 6.196 |
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) | |||||||||||
0.99 | 1.03 | 96.9 | 0.445 | 2.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | 0.99 | 15 | 56874 | 56874 | 1437 | 0.113 | 0.146 | 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 |
60 | 901.7 | 1107.68 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.089 |
s_zero_chiral_vol | 0.08 |
s_approx_iso_adps | 0.078 |
s_similar_adp_cmpnt | 0.045 |
s_anti_bump_dis_restr | 0.039 |
s_angle_d | 0.03 |
s_from_restr_planes | 0.0264 |
s_bond_d | 0.014 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1108 |
Nucleic Acid Atoms | |
Solvent Atoms | 242 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
SHELX | model building |
SHELXL-97 | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |