1O7H
NAPHTHALENE 1,2-DIOXYGENASE WITH OXIDIZED RIESKE IRON SULPHUR CENTER SITE.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1EG9 | PDB ENTRY 1EG9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6 | AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.56 | 52 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 138.308 | ¦Á = 90 |
b = 138.308 | ¦Â = 90 |
c = 206.67 | ¦Ã = 120 |
Symmetry | |
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Space Group | H 3 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 | CHESS 80MM | 1999-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
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 | 2.2 | 30 | 98 | 0.074 | 16 | 4.18 | 37958 |
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 | 2.25 | 98.6 | 0.363 |
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-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1EG9 | 2.2 | 30 | 36554 | 1925 | 99.4 | 0.208 | 0.242 | RANDOM | 22.83 |
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] | |
0.2 | 0.1 | 0.2 | -0.3 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 16.4 |
r_dihedral_angle_1_deg | 4.19 |
r_scangle_it | 3.639 |
r_scbond_it | 2.295 |
r_angle_refined_deg | 1.522 |
r_mcangle_it | 1.493 |
r_mcbond_it | 0.806 |
r_symmetry_hbond_refined | 0.559 |
r_nbd_refined | 0.227 |
r_symmetry_vdw_refined | 0.205 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5089 |
Nucleic Acid Atoms | |
Solvent Atoms | 358 |
Heterogen Atoms | 41 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |