3KH4
Crystal structure of human Cu/Zn superoxide dismutase recombinantly produced in Leishmania tarantolae; P6522 crystal form containing 6 chains in the asymmetric unit
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 292 | 21-25% (w/v) PEG4000, 0.1 M NaOAc, pH 4.2-5.2, vapor diffusion, hanging drop, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.1 | 69.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 112.188 | α = 90 |
b = 112.188 | β = 90 |
c = 428.268 | γ = 120 |
Symmetry | |
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Space Group | P 65 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 | MARMOSAIC 225 mm CCD | SI(111) | 2009-10-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X10SA | 1.0 | SLS | X10SA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 3.5 | 49.69 | 99.9 | 0.172 | 13.13 | 21168 | -3 | 47.084 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
3.5 | 3.6 | 100 | 0.586 | 4.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | THROUGHOUT | 3.5 | 49.69 | 21168 | 1088 | 99.92 | 0.201 | 0.201 | 0.208 | RANDOM | 90.385 |
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] | |
-8.44 | -4.22 | -8.44 | 12.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.163 |
r_dihedral_angle_3_deg | 18.979 |
r_dihedral_angle_4_deg | 11.035 |
r_dihedral_angle_1_deg | 7.179 |
r_angle_other_deg | 4.332 |
r_scangle_it | 2.63 |
r_angle_refined_deg | 1.434 |
r_scbond_it | 1.405 |
r_mcangle_it | 0.933 |
r_mcbond_it | 0.447 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6660 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |