2NT8
ATP bound at the active site of a PduO type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1NOG | PDB ENTRY 1NOG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH | 8.5 | 293 | 0.85 M Ammonium sulfate, 50 mM magnesium chloride, 150 mM sodium chloride, 1.5 mM ATP, 4 mM hydroxocobalamin, pH 8.5, BATCH, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.06 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 110.609 | α = 90 |
b = 110.609 | β = 90 |
c = 110.609 | γ = 90 |
Symmetry | |
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Space Group | I 2 3 |
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 | 2005-11-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 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 | 1.68 | 50 | 99.4 | 0.046 | 11.3 | 9.5 | 25595 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.68 | 1.74 | 99.4 | 0.234 | 0.234 | 4.1 | 6.8 | 2522 |
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 1NOG | 1.68 | 30 | 25595 | 1305 | 99.46 | 0.175 | 0.173 | 0.204 | RANDOM | 23.946 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.427 |
r_dihedral_angle_4_deg | 14.683 |
r_dihedral_angle_3_deg | 12.146 |
r_dihedral_angle_1_deg | 5.209 |
r_scangle_it | 3.699 |
r_scbond_it | 2.654 |
r_mcangle_it | 1.687 |
r_angle_refined_deg | 1.341 |
r_mcbond_it | 1.056 |
r_nbtor_refined | 0.304 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1440 |
Nucleic Acid Atoms | |
Solvent Atoms | 141 |
Heterogen Atoms | 49 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |