5UTU
2.65 Angstrom Resolution Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with SAH and NAD
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 295 | Protein: 9.3 mg/ml, 0.5M Sodium chloride, 0.1M Tris HCl (pH 8.3), 1mM Adenosine, 1mM NAD, 1mM Homocysteine; Screen: Classics II (F6), 0.2M Ammonium sulfate, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 107.906 | α = 90 |
b = 185.834 | β = 97.98 |
c = 121.619 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 225 mm CCD | C(111) | 2016-03-21 | 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) | 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 | 2.65 | 30 | 100 | 0.099 | 0.099 | 0.047 | 16.2 | 5.2 | 137384 | -3 | 58.5 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.65 | 2.7 | 100 | 0.646 | 0.646 | 0.307 | 0.843 | 2.8 | 5.2 |
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 | 5HM8 | 2.65 | 30 | 130306 | 6930 | 99.91 | 0.172 | 0.17041 | 0.20208 | RANDOM | 52.2 |
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] | |
0.74 | -0.55 | -2.47 | 1.82 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.326 |
r_dihedral_angle_4_deg | 13.195 |
r_dihedral_angle_3_deg | 11.373 |
r_long_range_B_refined | 5.86 |
r_long_range_B_other | 5.847 |
r_scangle_other | 3.796 |
r_mcangle_it | 3.187 |
r_mcangle_other | 3.187 |
r_dihedral_angle_1_deg | 2.643 |
r_scbond_it | 2.392 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 31128 |
Nucleic Acid Atoms | |
Solvent Atoms | 931 |
Heterogen Atoms | 837 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |