1OEV
Oxidation state of protein tyrosine phosphatase 1B
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1C83 | PDB ENTRY 1C83 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 12-18% PEG4000, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM ACETATE, 10MM DTT |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 59.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 88.245 | α = 90 |
b = 88.245 | β = 90 |
c = 104.656 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | RIGAKU CCD | CONFOCAL MULTILAYER OPTICS | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R |
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 | 2.2 | 76 | 96 | 0.06 | 11.2 | 2.24 | 23367 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.2 | 2.28 | 86.9 | 0.252 | 4.3 | 2.26 |
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 1C83 | 2.2 | 76.7 | 22178 | 1189 | 95.9 | 0.175 | 0.172 | 0.217 | RANDOM | 21.6 |
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] | |
0.75 | 0.37 | 0.75 | -1.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 6.014 |
r_scangle_it | 4.918 |
r_mcangle_it | 3.397 |
r_scbond_it | 3.188 |
r_mcbond_it | 2.108 |
r_angle_refined_deg | 1.211 |
r_angle_other_deg | 0.777 |
r_nbd_other | 0.241 |
r_symmetry_vdw_other | 0.232 |
r_nbd_refined | 0.193 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2292 |
Nucleic Acid Atoms | |
Solvent Atoms | 291 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
AMoRE | phasing |