2JI2
X-ray structure of E114A mutant of superoxide reductase from Desulfoarculus baarsii in the native, reduced form
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VZI | PDB ENTRY 1VZI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 293 | 16% PEG 4000, 100 MM TRIS/HNO3 PH9.0, 0.2 M CA(NO3)2 AND 25MG/ML PROTEIN MIXED 1:1 HANGING DROP VAPOUR DIFFUSION, 20 C, pH 9.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.47 | α = 90 |
b = 82.87 | β = 90 |
c = 201.95 | 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 CCD | MIRRORS | 2005-05-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 1.7 | 47.4 | 95.4 | 0.08 | 10.1 | 4.2 | 62357 | -3 | 21.3 |
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 | 1.7 | 1.8 | 82.8 | 0.34 | 4 | 3.9 |
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 | PDB ENTRY 1VZI | 1.7 | 47.4 | 62355 | 3155 | 95.4 | 0.195 | 0.195 | 0.222 | RANDOM | 24.8 |
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] | |
0.89 | -0.89 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 27.6 |
c_scangle_it | 3.05 |
c_mcangle_it | 2 |
c_scbond_it | 1.99 |
c_angle_deg | 1.3 |
c_mcbond_it | 1.26 |
c_improper_angle_d | 0.73 |
c_bond_d | 0.005 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3878 |
Nucleic Acid Atoms | |
Solvent Atoms | 568 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |