3IUN
apPEP_D622N opened state
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3IUJ | PDB entry 3IUJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 287 | 8mg/ml protein in 20mM Hepes (pH7.5), 100mM NaCl, 5% w/v glycerol, 1mM EDTA, and 1mM DTT. Equal volume of protein and precipitant (20mM MES (pH 6.5), 17% w/v PEG10K) were equilibrated by vapor diffusion at 14C. Cryosolution is precipitant plus 5% more PEG10K and 20% w/v glycerol., VAPOR DIFFUSION, temperature 287K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.92 | 57.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 62.81 | α = 90 |
b = 93.599 | β = 90 |
c = 152.896 | 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 | 100 | CCD | 2006-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.97934 | APS | 22-ID |
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 | 2.4 | 40 | 100 | 0.146 | 10.9 | 6.9 | 36350 | 36350 | -3 | -3 | 43.8 |
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) | |||||||||||
2.4 | 2.49 | 0.463 | 4.2 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 3IUJ | 2.4 | 39.92 | 35888 | 1879 | 99.5 | 0.206 | 0.206 | 0.25 | RANDOM | 49.9 |
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] | |
-0.74 | 13.72 | -12.98 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.6 |
c_scangle_it | 3.06 |
c_mcangle_it | 2.38 |
c_scbond_it | 2.08 |
c_mcbond_it | 1.44 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.71 |
c_bond_d | 0.006 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5306 |
Nucleic Acid Atoms | |
Solvent Atoms | 231 |
Heterogen Atoms | 6 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
EPMR | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |