3FXT
Crystal structure of the N-terminal domain of human NUDT6
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 19% PEG2000 MME, 0.1M Tris-HCl, 0.25M Trimethylamine. Chymotrypsin was added prior to crystallization to a ratio protease:protein of 1:100., pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
2 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 19% PEG2000 MME, 0.1M Tris-HCl, 0.3M Trimethylamine. Chymotrypsin was added prior to crystallization to a ratio protease:protein of 1:100. Crystal was then soaked for 17h in 10% PEG 2000MME, 0.1M Tris-HCl, 0.3M Trimethylamine and 1mM HgAc., pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
3 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 277 | 14% PEG2000 MME, 0.1M Tris-HCl. Chymotrypsin was added prior to crystallization to a ratio protease:protein of 1:100. Crystal was then soaked for 2weeks 10% PEG 2000MME, 0.1M Tris-HCl, 0.3M Trimethylamine and 1mM SmCl3., pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 185.8 | α = 90 |
b = 185.8 | β = 90 |
c = 129.2 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 64 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | ADSC QUANTUM Q315r | MIRRORS | 2008-11-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | 0.97931 | ESRF | ID29 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.3 | 99.5 | 0.091 | 0.115 | 17.09 | 7.05 | 58581 | 58279 | -3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.3 | 2.36 | 99.1 | 0.757 | 0.658 | 3.08 | 6.66 | 4241 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MIRAS | THROUGHOUT | 2.3 | 33.88 | -3 | 55426 | 55426 | 2957 | 100 | 0.20286 | 0.20286 | 0.20112 | 0.23539 | RANDOM | 11.082 |
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] | |
0.17 | 0.09 | 0.17 | -0.26 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.02 |
r_dihedral_angle_4_deg | 14.784 |
r_dihedral_angle_3_deg | 13.92 |
r_dihedral_angle_1_deg | 5.275 |
r_angle_other_deg | 2.199 |
r_scangle_it | 2.039 |
r_scbond_it | 1.157 |
r_angle_refined_deg | 1.022 |
r_mcangle_it | 0.998 |
r_mcbond_it | 0.52 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 5594 |
Nucleic Acid Atoms | |
Solvent Atoms | 354 |
Heterogen Atoms | 36 |
Software
Software | |
---|---|
Software Name | Purpose |
ADSC | data collection |
autoSHARP | phasing |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |