4HUT
Structure of ATP:co(I)rrinoid adenosyltransferase (CobA) from Salmonella enterica in complex with four and five-coordinate cob(II)alamin and ATP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 19.6% PEG4000, 320 mM NaCl, pH 6.0, vapor diffusion, hanging drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.862 | α = 90 |
b = 74.223 | β = 90 |
c = 92.396 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | SBC-3 | 2011-04-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.979 | APS | 19-BM |
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 | 1.95 | 50 | 98.4 | 0.091 | 11.6 | 4.7 | 30567 | 30078 | -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 | 1.95 | 1.98 | 99.8 | 0.732 | 4.8 | 1497 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1G5R | 1.95 | 29.87 | 30679 | 29962 | 1514 | 97.66 | 0.178 | 0.178 | 0.1752 | 0.2315 | RANDOM | 34.4362 |
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] | |
3.49 | -0.41 | -3.08 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.041 |
r_dihedral_angle_4_deg | 19.946 |
r_dihedral_angle_3_deg | 14.745 |
r_dihedral_angle_1_deg | 6.004 |
r_angle_refined_deg | 2.208 |
r_chiral_restr | 0.147 |
r_bond_refined_d | 0.02 |
r_gen_planes_refined | 0.011 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2762 |
Nucleic Acid Atoms | |
Solvent Atoms | 323 |
Heterogen Atoms | 227 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data collection |
HKL-3000 | data reduction |
MOLREP | phasing |