1YDH
X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene at5g11950
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | 293 | 10 MG/ML PROTEIN, 13% MPEG 2K, 0.28 M POTASSIUM NITRATE, 0.1 M MOPS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.63 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 121.589 | ¦Á = 90 |
b = 80.427 | ¦Â = 102.97 |
c = 50.709 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | APS-1 | SAGITALLY FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR | 2004-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | APS | 19-BM |
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 | 2.152 | 35.451 | 99.9 | 0.384 | 6.266 | 6.9 | 25771 |
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) | |||||||||||
2.15 | 2.23 | 100 | 0.384 | 2.401 | 6.2 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.152 | 35.45 | 25679 | 1300 | 99.1 | 0.16164 | 0.16164 | 0.159 | 0.213 | RANDOM | 31.14 |
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] | |
0.915 | 0.386 | -0.158 | -0.584 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.733 |
r_dihedral_angle_4_deg | 21.845 |
r_dihedral_angle_3_deg | 14.836 |
r_scangle_it | 6.985 |
r_dihedral_angle_1_deg | 5.547 |
r_scbond_it | 5.121 |
r_mcangle_it | 2.656 |
r_angle_refined_deg | 1.939 |
r_mcbond_it | 1.579 |
r_nbtor_refined | 0.302 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2798 |
Nucleic Acid Atoms | |
Solvent Atoms | 319 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
SOLVE | phasing |
RESOLVE | phasing |
REFMAC | refinement |