6X7U
Crystal Structure of the Human Nudix Hydrolase Nudt16 in complex with FAD
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M ammonium chloride and 20% (w/v) PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 47.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.721 | α = 90 |
b = 64.721 | β = 90 |
c = 77.751 | γ = 120 |
Symmetry | |
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Space Group | P 32 |
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 | 2018-10-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97910 | APS | 24-ID-C |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.7 | 45.5 | 99.5 | 0.096 | 0.996 | 11.4 | 4.3 | 9929 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.7 | 2.87 | 0.602 | 1.65 |
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 | 3COU | 2.7 | 45.47 | 9480 | 448 | 99.52 | 0.1619 | 0.1587 | 0.2313 | RANDOM | 56.583 |
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] | |
2.01 | 2.01 | -4.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.839 |
r_dihedral_angle_3_deg | 18.355 |
r_dihedral_angle_4_deg | 15.161 |
r_dihedral_angle_1_deg | 7.727 |
r_angle_refined_deg | 1.498 |
r_angle_other_deg | 1.151 |
r_chiral_restr | 0.054 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2524 |
Nucleic Acid Atoms | |
Solvent Atoms | 36 |
Heterogen Atoms | 80 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data scaling |
PHASER | phasing |