5DK6
CRYSTAL STRUCTURE OF A 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE (MTA/SAH) NUCLEOSIDASE (MTAN) FROM COLWELLIA PSYCHRERYTHRAEA 34H (CPS_4743, TARGET PSI-029300) IN COMPLEX WITH ADENINE AT 2.27 A RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 292 | Protein (37.95 mg/ml, 20 mM HEPES pH 7.5, 150 mM Sodium Chloride, 5% v/v Glycerol, 5 mM DTT) were combined with an equal volume of Reservoir (100 mM Bicine pH 8.0, 1.98 M Ammonium Sulfate, 135 mM Sodium Succinate, 4 mM Glycine, 15 mM CYMAL-7); Cryoprotection (75 mM Bicine pH 8.0, 1.49 M Ammonium Sulfate, 101 mM Sodium Succinate, 3 mM Glycine, 11 mM CYMAL-7) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.84 | 68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 145.427 | α = 90 |
b = 145.427 | β = 90 |
c = 70.341 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 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 | RAYONIX MX225HE | MIRRORS | 2013-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.97931 | APS | 31-ID |
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 | 2.268 | 26 | 96.4 | 0.1 | 11.5 | 3.9 | 37023 | -0.3 | 33.16 |
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 | 2.27 | 2.36 | 82.8 | 0.337 | 2.148 | 2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | FREE R-VALUE | 2.27 | 25.28 | 1.45 | 20433 | 1002 | 98.2 | 0.21 | 0.2082 | 0.2371 | Random | 43.6 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 18.474 |
f_angle_d | 1.201 |
f_chiral_restr | 0.043 |
f_bond_d | 0.01 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1802 |
Nucleic Acid Atoms | |
Solvent Atoms | 101 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data collection |
SCALEPACK | data scaling |
PDB_EXTRACT | data extraction |
PHENIX | phasing |
HKL-2000 | data reduction |