3QCE
Human receptor protein tyrosine phosphatase gamma, domain 1, in complex with 3-[(3,4-dichlorobenzyl)sulfanyl]thiophene-2-carboxylic acid via soaking
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3QCB | PDB ENTRY 3QCB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 277 | pH 6.5, vapor diffusion, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.9 | α = 90 |
b = 82.5 | β = 90 |
c = 127 | 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 | ADSC QUANTUM 210 | 2005-12-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0 | APS | 17-ID |
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 | 2.1 | 50 | 99.9 | 0.087 | 21.5 | 7.2 | 46575 | 20.2 |
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 | 2.1 | 2.18 | 100 | 0.578 | 3.7 | 7.3 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3QCB | 2.1 | 31.41 | 46385 | 46385 | 682 | 99.3 | 0.234 | 0.233 | 0.261 | RANDOM | 33.3288 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
3.73 | 1.31 | -5.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 21.1 |
c_scangle_it | 3.14 |
c_mcangle_it | 2.36 |
c_scbond_it | 2.14 |
c_mcbond_it | 1.51 |
c_angle_deg | 1.3 |
c_improper_angle_d | 0.65 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4561 |
Nucleic Acid Atoms | |
Solvent Atoms | 164 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
PDB_EXTRACT | data extraction |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
CNX | refinement |