5JCG
Structure of Human Peroxiredoxin 3 as three stacked rings
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZYE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 293 | 12.5% PEG1000, 12.5% PEG3350. 12.5% MPD, 0.02 M alcohol additives at pH 8.5 (Gorrec, 2009) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.21 | 61.69 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 133.188 | α = 90 |
b = 168.73 | β = 90 |
c = 221.55 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | ADSC QUANTUM 315 | 2015-04-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.979 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 2.8 | 52.27 | 99.8 | 0.176 | 0.954 | 6.6 | 12.7 | 61455 |
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) | |||||||||||
1 | 2.8 | 2.87 | 99.7 | 0.713 | 12.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1ZYE | 2.8 | 52.27 | 58445 | 3005 | 99.7 | 0.1849 | 0.1826 | 0.2288 | RANDOM | 22.738 |
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] | |
-1.15 | 1.8 | -0.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.219 |
r_dihedral_angle_4_deg | 15.771 |
r_dihedral_angle_3_deg | 15.124 |
r_dihedral_angle_1_deg | 6.389 |
r_mcangle_it | 1.587 |
r_angle_refined_deg | 1.378 |
r_angle_other_deg | 0.939 |
r_mcbond_it | 0.897 |
r_mcbond_other | 0.897 |
r_chiral_restr | 0.079 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 13658 |
Nucleic Acid Atoms | |
Solvent Atoms | 159 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |