2H6Z
Crystal Structure of Thioredoxin Mutant E44D in Hexagonal (p61) Space Group
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2TRX | pdb entry 2TRX |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | COUNTER-DIFFUSION | 3.5 | 277 | 60% (v/v) MPD, Ac2Cu 1 mM, 15mM Hepes pH 7.0, pH 3.5, Counter-diffusion, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.916 | α = 90 |
b = 102.916 | β = 90 |
c = 42.559 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 | BRUKER SMART 6000 | Montel Optics | 2005-12-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | OTHER | 1.5418 |
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 | 2.25 | 51.46 | 99.9 | 0.022 | 29.91 | 21.63 | 12447 | 12447 | 44.395 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.25 | 2.3 | 100 | 0.2079 | 3.59 | 12.91 | 786 |
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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 2TRX | 2.25 | 51.434 | 12446 | 12038 | 1180 | 96.761 | 0.234 | 0.234 | 0.228 | 0.2901 | random | 43.103 |
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] | |
-0.759 | -0.379 | -0.759 | 1.138 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.034 |
r_dihedral_angle_3_deg | 14.725 |
r_dihedral_angle_4_deg | 12.176 |
r_dihedral_angle_1_deg | 6.213 |
r_mcangle_it | 1.889 |
r_scangle_it | 1.619 |
r_angle_refined_deg | 1.303 |
r_mcbond_it | 1.193 |
r_scbond_it | 1.121 |
r_nbtor_refined | 0.303 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1627 |
Nucleic Acid Atoms | |
Solvent Atoms | 97 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
SAINT | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PROTEUM PLUS | data reduction |
SADABS | data scaling |
XPREP | data reduction |
Coot | model building |
MolProbity | model building |