Cyanophage S-2L HD phosphohydrolase (DatZ) bound to dA and one catalytic Zn2+ ion
Serial Crystallography (SX)
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 291.15 | 1.5 M LiSO4; 100 mM HEPES |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.5 | 50.89 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 141.489 | α = 90 |
b = 141.489 | β = 90 |
c = 53.601 | γ = 120 |
Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 9M | KB Mirrors | 2018-11-30 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 0.729309 | SOLEIL | PROXIMA 2 |
Serial Crystallography
Sample delivery method |
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Diffraction ID | Description | Sample Delivery Method |
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1 | | fixed target |
Data Reduction |
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Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
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1 | | 1 | | |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 |
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1 | 0.86 | 49.11 | 100 | 0.105 | 0.105 | 0.013 | 1 | 27.6 | 61.2 | | 172371 | | | 7.42892855759 |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 0.86 | 0.87 | 100 | | 4.749 | 4.796 | 0.667 | 0.689 | 1.7 | 51.8 | |
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 | Mean Isotropic B |
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X-RAY DIFFRACTION | SAD | FREE R-VALUE | 0.860002552904 | 40.8443561187 | 1.33649116274 | 172344 | 8593 | 99.9860763019 | 0.129509197469 | 0.129225627388 | 0.134769670725 | 21.2059493131 |
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] |
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| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 17.429674008 |
f_angle_d | 0.945230405214 |
f_chiral_restr | 0.0646888183896 |
f_plane_restr | 0.00950995085662 |
f_bond_d | 0.00591732709658 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1395 |
Nucleic Acid Atoms | |
Solvent Atoms | 218 |
Heterogen Atoms | 20 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
SHELXCD | phasing |