3R0X
Crystal structure of Selenomethionine incorporated apo D-serine deaminase from Salmonella tyhimurium
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.1 | 298 | 0.1M Trisodium citrate pH 6.1, 0.4M Ammonium sulphatem, 0.8M Lithium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.52 | 51.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.46 | α = 90 |
b = 188.39 | β = 90 |
c = 46.59 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 225 mm CCD | 2009-10-28 | M | MAD | ||||||
2 | 1 | x-ray | 100 | IMAGE PLATE | MAR scanner 345 mm plate | 2009-11-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 0.97848, 0.97872, 1.01876, 0.97083 | ESRF | BM14 |
2 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.93 | 48.4 | 93.7 | 0.053 | 28.2 | 9.1 | 36067 | 14.7 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.9 | 2 | 82.5 | 0.174 | 12 | 10.1 | 4560 |
Refinement
Statistics | |||||||||||||||||||
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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 | 1.93 | 36.17 | 34192 | 1822 | 94.37 | 0.18212 | 0.18063 | 0.20986 | RANDOM | 15.799 |
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] | |
0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.541 |
r_dihedral_angle_4_deg | 15.155 |
r_dihedral_angle_3_deg | 12.638 |
r_dihedral_angle_1_deg | 4.8 |
r_scangle_it | 1.332 |
r_angle_refined_deg | 0.915 |
r_scbond_it | 0.83 |
r_mcangle_it | 0.565 |
r_mcbond_it | 0.294 |
r_chiral_restr | 0.061 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3291 |
Nucleic Acid Atoms | |
Solvent Atoms | 387 |
Heterogen Atoms | 36 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
Auto-Rickshaw | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |