2PWJ
Structure of a mitochondrial type II peroxiredoxin from Pisum sativum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 293 | PEG2000, citrate, NaCl, DTT, 2-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.88 | α = 102.94 |
b = 66.4 | β = 104.44 |
c = 77.23 | γ = 99.07 |
Symmetry | |
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Space Group | P 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 | BRUKER PLATINUM 200 | Microstar micro-focus | 2005-02-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR-H |
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 | 2.39 | 71.9 | 65.79 | 0.067 | 15.416 | 3.08 | 30073 | 30073 | 22.1 |
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) | |||||||||||
2.4 | 2.48 | 0.078 |
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-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | model generated by EasyPed3D Web Server 1.0 | 2.8 | 14.98 | 27653 | 25728 | 2544 | 93 | 0.298 | 0.298 | 0.277 | 0.292 | RANDOM | 14.29 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
7.53 | -4.01 | 5.77 | -5.66 | -0.18 | -1.87 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_torsion_deg | 23.7 |
x_scangle_it | 2.17 |
x_angle_deg | 1.9 |
x_mcangle_it | 1.65 |
x_scbond_it | 1.41 |
x_mcbond_it | 0.97 |
x_torsion_impr_deg | 0.93 |
x_bond_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7476 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
SAINT | data scaling |
AMoRE | phasing |
CNS | refinement |
PDB_EXTRACT | data extraction |
PROTEUM PLUS | data collection |
SAINT | data reduction |
XPREP | data reduction |