1MT1
The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannaschii
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | PEG 2000, 2-methyl-2,4-pentanediol, glycerol, n-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid], beta octyl glucoside, putrescine, ethylenediaminetetraacetic acid dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.12 | 42.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.77 | α = 90 |
b = 92.99 | β = 94.84 |
c = 87.23 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | ADSC QUANTUM 315 | 2002-04-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 8-BM | 0.9793 | APS | 8-BM |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.11 | 63.5 | 99.9 | 0.142 | 4.1 | 6.9 | 57557 | 57557 | 14.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.11 | 2.24 | 100 | 0.383 | 1.6 | 6.9 | 8398 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | none | 2.2 | 63.5 | 89997 | 89997 | 8839 | 99.7 | 0.206 | 0.19 | 0.19 | 0.229 | RANDOM | 19.5 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-3.84 | -1.43 | 9.83 | -5.99 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.9 |
c_scangle_it | 4.18 |
c_scbond_it | 2.84 |
c_mcangle_it | 2.23 |
c_mcbond_it | 1.41 |
c_angle_deg | 1.3 |
c_improper_angle_d | 1.13 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7469 |
Nucleic Acid Atoms | |
Solvent Atoms | 454 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SnB | phasing |
SOLVE | phasing |
OASIS | model building |
CNS | refinement |
CCP4 | data scaling |
OASIS | phasing |
CNS | phasing |