2G40
Crystal structure of a duf162 family protein (dr_1909) from deinococcus radiodurans at 1.70 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 8.3 | 277 | 20.0% PEG-3350, 0.2M K3Citrate, No Buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
2 | VAPOR DIFFUSION, SITTING DROP, NANODROP | 7.5 | 277 | 0.2M MgCl2, 30.0% PEG-400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.41 | α = 90 |
b = 53.41 | β = 90 |
c = 118.31 | 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 QUANTUM 4 | 2004-08-26 | M | SINGLE WAVELENGTH | ||||||
2 | 2 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing | 2006-01-12 | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.3 | ALS | 5.0.3 | |
2 | SYNCHROTRON | SSRL BEAMLINE BL1-5 | 0.918381, 0.979310, 0.978359 | SSRL | BL1-5 |
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 | 1.7 | 27.28 | 98.3 | 0.067 | 18.38 | 19674 | 25.34 |
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 | 1.7 | 1.76 | 94.7 | 0.498 | 2.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.7 | 27.28 | 19611 | 984 | 99.79 | 0.18 | 0.178 | 0.22 | RANDOM | 19.501 |
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] | |
-0.28 | -0.28 | 0.57 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 40.646 |
r_dihedral_angle_4_deg | 19.185 |
r_dihedral_angle_3_deg | 10.805 |
r_dihedral_angle_1_deg | 6.218 |
r_scangle_it | 5.939 |
r_scbond_it | 4.089 |
r_mcangle_it | 2.317 |
r_mcbond_it | 1.716 |
r_angle_refined_deg | 1.344 |
r_angle_other_deg | 0.78 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1216 |
Nucleic Acid Atoms | |
Solvent Atoms | 132 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHARP | phasing |