1GN9
Hybrid Cluster Protein from Desulfovibrio desulfuricans ATCC 27774 X-ray structure at 2.6A resolution using synchrotron radiation at a wavelength of 1.722A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1E2U | PDB FROM ENTRY 1E2U, EXCLUDING ALL CLUSTER ATOMS AND SOLVENT MOLECULES |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6 | 293 | 25% PEG 4000, 0.1M MES PH6.0, T=293K, pH 6.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.4 | α = 82.7 |
b = 61.8 | β = 73.7 |
c = 72.2 | γ = 87.3 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | COLLIMATING AND FOCUSING MIRROR | 2000-11-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.6 | 30 | 95.9 | 0.08 | 4.2 | 4.1 | 27761 | 18.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.6 | 2.69 | 94.5 | 0.13 | 2.6 | 4.1 |
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 | IRON ANOMALOUS AND MOLECULAR REPLACEMENT | THROUGHOUT | PDB FROM ENTRY 1E2U, EXCLUDING ALL CLUSTER ATOMS AND SOLVENT MOLECULES | 2.6 | 25.01 | 27982 | 732 | 96.3 | 0.193 | 0.193 | 0.26 | RANDOM | 10.9 |
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] | |
0.73 | 0.12 | -2.94 | -0.38 | 0.4 | -0.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.3 |
c_scangle_it | 5.38 |
c_mcangle_it | 4.64 |
c_scbond_it | 3.79 |
c_mcbond_it | 2.99 |
c_improper_angle_d | 2.38 |
c_angle_deg | 1.3 |
c_bond_d | 0.013 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8173 |
Nucleic Acid Atoms | |
Solvent Atoms | 200 |
Heterogen Atoms | 31 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALA | data scaling |
AMoRE | phasing |