7R7J
Crystal structure of RadD with ADP
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.7 | 277 | 20 mM Tris-HCl, 100 mM potassium chloride, 0.5 mM DTT, 0.5 mM magnesium chloride, 0.5 mM ATPgS, 9% (w/v) PEG 3350, 75 mM sodium thiocyanate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.71 | 54.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.415 | α = 84.659 |
b = 74.449 | β = 80.028 |
c = 109.4 | γ = 82.769 |
Symmetry | |
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Space Group | P 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 | 2019-06-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.97856 | APS | 21-ID-D |
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 | |||||
1 | 2.03 | 45 | 90.5 | 0.105 | 0.124 | 0.066 | 0.983 | 10.1 | 3.3 | 79347 | 33.23 |
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) | ||||||||
1 | 2.03 | 2.1 | 60.7 | 1.105 | 1.378 | 0.81 | 0.39 | 0.1 | 2.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6DJE | 2.03 | 35.65 | 0.08 | 71229 | 1812 | 80.96 | 0.2373 | 0.2364 | 0.2694 | 54.13 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 9.1549 |
f_angle_d | 0.608 |
f_chiral_restr | 0.0417 |
f_plane_restr | 0.0047 |
f_bond_d | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8846 |
Nucleic Acid Atoms | |
Solvent Atoms | 286 |
Heterogen Atoms | 60 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHENIX | phasing |
PHENIX | refinement |