3EPB
Human AdoMetDC E256Q mutant complexed with putrescine
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1I7B |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 295 | 16% PEG 8000, 100 mM Tris, 10 mM DTT, pH 8.0, vapor diffusion, hanging drop, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 47.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.351 | α = 90 |
b = 53.54 | β = 109.09 |
c = 74.709 | γ = 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 | ADSC QUANTUM 315 | 2007-03-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.9792 | APS | 24-ID-E |
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 | 1.75 | 50 | 97.7 | 0.042 | 0.042 | 30.146 | 3.6 | 34072 | 33438 | 24.2 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||||
1.75 | 1.81 | 89.6 | 0.158 | 0.158 | 4.6 | 3 | 3110 |
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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1I7B | 1.75 | 35.3 | 34072 | 33438 | 3341 | 95.6 | 0.238 | 0.238 | 0.238 | 0.253 | RANDOM | 31.517 |
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] | |
1.38 | 1.32 | 6.74 | -8.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 26.4 |
c_scangle_it | 2.81 |
c_mcangle_it | 2.19 |
c_scbond_it | 1.89 |
c_angle_deg | 1.5 |
c_mcbond_it | 1.33 |
c_improper_angle_d | 1.29 |
c_bond_d | 0.016 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2489 |
Nucleic Acid Atoms | |
Solvent Atoms | 194 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | refinement |
PDB_EXTRACT | data extraction |
ADSC | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |