5LW6
Crystal structure of a Se-Met substituted Dictyostelium discoideum ADP-ribose binding macrodomain (residues 342-563) of DDB_G0293866
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 294 | Crystallization trials were performed with proteins at 25 mg/ml in buffer containing 150 mM NaCl, 1 mM DTT and 25 mM Tris-HCl (pH 7.5), at 20 C with commercial screens using the sitting-drop vapour-diffusion method. Crystallization drops were set up with the aid of a Mosquito Crystal robot (TTP Labtech) using 200 nl of protein solution plus 200 nl of reservoir solution in MRC two-well crystallization microplates (Swissci) equilibrated against 75 microl of reservoir solution. Co-crystallisation trials were set up by adding 2 mM ADPr to the protein for at least 1 hour prior to setting up crystallisation drops. Crystals of the macrodomain proteins grew in 0.2 M Lithium sulphate, 0.1 M phosphate/citrate and 20% (w/v) PEG1000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.98 | 37.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.59 | α = 90 |
b = 71.22 | β = 90 |
c = 81.89 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | PIXEL | DECTRIS PILATUS 6M-F | 2013-05-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.97 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.8 | 25.19 | 99.9 | 0.078 | 17.3 | 25.8 | 22050 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.8 | 1.85 | 100 | 0.943 | 5.3 | 25.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.8 | 25.19 | 20867 | 1131 | 99.91 | 0.17205 | 0.16982 | 0.21433 | RANDOM | 19.915 |
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] | |
-0.01 | 0.02 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.835 |
r_dihedral_angle_3_deg | 14.138 |
r_dihedral_angle_4_deg | 11.446 |
r_dihedral_angle_1_deg | 6.14 |
r_angle_refined_deg | 1.898 |
r_angle_other_deg | 0.908 |
r_chiral_restr | 0.118 |
r_bond_refined_d | 0.02 |
r_gen_planes_refined | 0.01 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1786 |
Nucleic Acid Atoms | |
Solvent Atoms | 103 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
MLPHARE | phasing |