3DTV
Crystal structure of arylmalonate decarboxylase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 293 | 1.5M ammonium sulfate, 12%(W/V) glycerol, 0.1M Tris-HCl pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57.58 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 82.63 | ¦Á = 90 |
b = 99.321 | ¦Â = 90 |
c = 140.263 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | ADSC QUANTUM 210 | TOROIDAL MIRROR | 2007-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44B2 | SPring-8 | BL44B2 |
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 | 50 | 99.7 | 0.048 | 32.4 | 7.2 | 68279 | 1 |
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 | 2.14 | 98.2 | 0.327 | 4.5 |
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 | MIR | THROUGHOUT | 2.1 | 20 | 64363 | 3386 | 99.7 | 0.195 | 0.193 | 0.241 | RANDOM | 47.03 |
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] | |
1.63 | -0.36 | -1.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.24 |
r_dihedral_angle_4_deg | 21.876 |
r_dihedral_angle_3_deg | 18.658 |
r_dihedral_angle_1_deg | 6.77 |
r_scangle_it | 4.856 |
r_mcangle_it | 4.176 |
r_scbond_it | 3.644 |
r_mcbond_it | 2.961 |
r_angle_refined_deg | 1.553 |
r_nbtor_refined | 0.315 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6628 |
Nucleic Acid Atoms | |
Solvent Atoms | 363 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
DM | model building |
MLPHARE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |