5T8K
1.95 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenine and NAD
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5HM8 | PDB-5HM8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 292 | Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3), 1mM Adenine, 1mM NAD, 1mM Homocysteine, Screen: Classics II (D9), 0.1M Bis-Tris-HCL (pH 8.5), 25% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 52.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.686 | α = 90 |
b = 182.785 | β = 100.58 |
c = 96.25 | 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 300 mm CCD | C(111) | 2016-06-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 30 | 100 | 0.076 | 0.076 | 20.8 | 3.8 | 166729 | -3 | 26 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.95 | 1.98 | 100 | 0.722 | 0.65 | 2 | 3.7 |
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-5HM8 | 1.95 | 29.92 | 158251 | 8283 | 99.93 | 0.1425 | 0.14092 | 0.17296 | RANDOM | 33.031 |
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] | |
-0.58 | -0.47 | 0.14 | 0.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.292 |
r_dihedral_angle_3_deg | 10.082 |
r_dihedral_angle_4_deg | 8.183 |
r_long_range_B_refined | 5.741 |
r_long_range_B_other | 5.473 |
r_dihedral_angle_1_deg | 3.175 |
r_scangle_other | 2.641 |
r_mcangle_it | 2.158 |
r_mcangle_other | 2.157 |
r_scbond_it | 1.588 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 15562 |
Nucleic Acid Atoms | |
Solvent Atoms | 1925 |
Heterogen Atoms | 364 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |