1VR7
Crystal structure of S-adenosylmethionine decarboxylase proenzyme (TM0655) from THERMOTOGA MARITIMA at 1.2 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 277 | 1.0M LiCl, 10.0% PEG-6000, 0.1M TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.298 | α = 90 |
b = 105.298 | β = 90 |
c = 69.427 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | 2005-01-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | ALS | 8.3.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.2 | 55.24 | 99 | 0.055 | 0.055 | 7.1 | 3 | 88939 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.2 | 1.23 | 93.5 | 0.575 | 0.575 | 1.2 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | FREE R | 1.2 | 55 | 88936 | 4307 | 99 | 0.12 | 0.15 | RANDOM | 22.152 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
11 | 1716 | 2083 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_approx_iso_adps | 0.09 |
s_zero_chiral_vol | 0.081 |
s_non_zero_chiral_vol | 0.08 |
s_similar_adp_cmpnt | 0.062 |
s_anti_bump_dis_restr | 0.049 |
s_angle_d | 0.035 |
s_from_restr_planes | 0.03 |
s_bond_d | 0.015 |
s_rigid_bond_adp_cmpnt | 0.005 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1924 |
Nucleic Acid Atoms | |
Solvent Atoms | 153 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
SHELX | refinement |
SCALA | data scaling |
MOSFLM | data reduction |
CCP4 | data scaling |
CNS | phasing |
SHELXL-97 | refinement |