5J07
Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, circular permutant P1/2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4BCZ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 5 | 293 | 0.1 M MIB buffer pH 5.0 25 % w/v PEG 1500 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 41.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 75.04 | α = 90 |
b = 75.04 | β = 90 |
c = 59.01 | γ = 120 |
Symmetry | |
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Space Group | P 65 |
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 | MARRESEARCH | 2014-09-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-3 | 1 | MAX II | I911-3 |
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 | 40 | 100 | 0.095 | 15.2 | 12.2 | 12893 |
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) | |||||||||||
1 | 2 | 2.05 | 0.618 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 4bcz | 2 | 32.51 | 12221 | 644 | 99.95 | 0.1946 | 0.1927 | 0.2306 | RANDOM | 49.806 |
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] | |
0.96 | 0.96 | 0.96 | -3.11 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 49.725 |
r_dihedral_angle_2_deg | 36.771 |
r_sphericity_bonded | 32.341 |
r_dihedral_angle_3_deg | 11.253 |
r_dihedral_angle_4_deg | 9.748 |
r_rigid_bond_restr | 7.113 |
r_dihedral_angle_1_deg | 4.755 |
r_mcangle_it | 4.112 |
r_mcbond_it | 3.174 |
r_mcbond_other | 3.169 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1595 |
Nucleic Acid Atoms | |
Solvent Atoms | 85 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |
MOLREP | phasing |