6PO4
2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (mtnN) from Haemophilus influenzae PittII.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.3 | 295 | Protein: 14.5 mg/ml, 0.01M Tris pH 8.3; Screen: Classics II (B5), 1.26M Sodium phosphate, 0.14M Potassium phosphate; Cryo: 1:1, reservoir : 50% Sucrose. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.35 | 63.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 124.536 | α = 90 |
b = 214.743 | β = 90 |
c = 146.904 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | MARMOSAIC 300 mm CCD | C(111) | 2017-07-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 2.1 | 30 | 100 | 0.081 | 0.081 | 0.089 | 0.035 | 19.8 | 6.2 | 115902 | -3 | 38.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 2.1 | 2.14 | 100 | 0.74 | 0.74 | 0.806 | 0.318 | 0.807 | 2.7 | 6.3 |
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 | 3o4v | 2.1 | 29.87 | 108746 | 5621 | 99.92 | 0.1618 | 0.1603 | 0.1907 | RANDOM | 44.826 |
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] | |
-0.8 | -2.38 | 3.18 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.623 |
r_dihedral_angle_4_deg | 14.198 |
r_dihedral_angle_3_deg | 10.014 |
r_dihedral_angle_1_deg | 4.116 |
r_angle_refined_deg | 1.363 |
r_angle_other_deg | 0.325 |
r_gen_planes_refined | 0.057 |
r_gen_planes_other | 0.056 |
r_chiral_restr | 0.055 |
r_bond_refined_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10256 |
Nucleic Acid Atoms | |
Solvent Atoms | 784 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MoRDa | phasing |