3IU0
Structural basis for zymogen activation and substrate binding of transglutaminase from Streptomyces mobaraense
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1IU4 | PDB ENTRY 1IU4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 293 | 30% PEG8000, 50mM NaCl, 1mM EDTA, 1mM beta-mercaptoethanol, 0.01% NaN3, 100mM cacodylic acid, pH5.0 and 2% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 64.333 | α = 90 |
b = 67.123 | β = 90 |
c = 83.969 | γ = 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 | 180 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R | 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 | 1.9 | 20 | 100 | 0.043 | 39.2 | 8.2 | 29327 | -3 | 27.7 |
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) | ||||||||||
1.9 | 1.99 | 99.9 | 0.238 | 0.238 | 8.1 | 8 | 3592 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1IU4 | 1.9 | 19.129 | 26318 | 2953 | 99.99 | 0.213 | 0.21319 | 0.20971 | 0.24394 | RANDOM | 28.615 |
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] | |
0.015 | 0.004 | -0.019 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.947 |
r_dihedral_angle_4_deg | 14.94 |
r_dihedral_angle_3_deg | 14.278 |
r_dihedral_angle_1_deg | 5.142 |
r_scangle_it | 2.579 |
r_scbond_it | 1.554 |
r_angle_refined_deg | 1.056 |
r_mcangle_it | 1.017 |
r_mcbond_it | 0.542 |
r_nbtor_refined | 0.299 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2777 |
Nucleic Acid Atoms | |
Solvent Atoms | 150 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
MOLREP | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |