2W4E
Structure of an N-terminally truncated Nudix hydrolase DR2204 from Deinococcus radiodurans
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7 | 0.2 M LINO3 20% W/V POLYETHYLENE GLYCOL 3350, pH 7 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.59 | 52 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.301 | α = 90 |
b = 61.301 | β = 90 |
c = 165.752 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 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 CCD | TOROIDAL MIRROR | 2008-09-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 50 | 99.7 | 0.08 | 11 | 4.4 | 22215 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.11 | 100 | 0.39 | 3.6 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | SAD | THROUGHOUT | NONE | 2 | 57.45 | 21034 | 1134 | 99.6 | 0.21 | 0.208 | 0.247 | RANDOM | 33.12 |
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] | |
-0.38 | -0.38 | 0.77 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.957 |
r_dihedral_angle_4_deg | 18.673 |
r_dihedral_angle_3_deg | 15.592 |
r_dihedral_angle_1_deg | 6.25 |
r_scangle_it | 3.971 |
r_scbond_it | 2.4 |
r_mcangle_it | 1.652 |
r_angle_refined_deg | 1.583 |
r_mcbond_it | 0.967 |
r_chiral_restr | 0.103 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2027 |
Nucleic Acid Atoms | |
Solvent Atoms | 144 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | phasing |
SHARP | phasing |
REFMAC | refinement |