2A03
Superoxide dismutase protein from plasmodium berghei
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ISC | pdb entry 1ISC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | 277 | 0.4 ul protein 20 mg/ml, 0.4 ul crystallization buffer, 100mM Zn acetate, 14% PEG 8000, 80mM Na citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.51 | 64.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.111 | α = 90 |
b = 105.111 | β = 90 |
c = 207.935 | 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 | ADSC QUANTUM 315 | 2005-03-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.9537 | ALS | 8.2.2 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.33 | 50 | 98.7 | 0.084 | 25.704 | 12.9 | 29521 |
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 | 2.33 | 2.41 | 86.8 | 0.465 | 2.952 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | pdb entry 1ISC | 2.33 | 20 | 29383 | 1493 | 98.963 | 0.1707 | 0.2017 | random | 28.207 |
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] | |
1.332 | 0.666 | 1.332 | -1.997 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.826 |
r_dihedral_angle_3_deg | 12.662 |
r_dihedral_angle_4_deg | 6.173 |
r_dihedral_angle_1_deg | 5.484 |
r_scangle_it | 2.641 |
r_scbond_it | 1.888 |
r_mcangle_it | 1.175 |
r_scangle_other | 1.091 |
r_angle_refined_deg | 1.087 |
r_mcbond_it | 0.896 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3133 |
Nucleic Acid Atoms | |
Solvent Atoms | 256 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
EPMR | phasing |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |