2I3U
Structural studies of protein tyrosine phosphatase beta catalytic domain in complex with inhibitors
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2I3R | PDB ENTRY 2I3R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 278 | 21% PEG 8000, 220 mM MgCl2, 1% BME, 0.1% BOG, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.785 | α = 90 |
b = 69.777 | β = 90 |
c = 118.523 | 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 | MARRESEARCH | Si monochromator | 2004-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-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 | 1.85 | 22.31 | 98.2 | 0.028 | 21.75 | 4.5 | 27971 | 27971 | 26.4 |
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 | 1.85 | 1.95 | 93.3 | 0.19 | 5.11 | 3.5 | 3939 |
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 2I3R | 1.85 | 22.31 | 27925 | 27925 | 1409 | 98.34 | 0.187 | 0.187 | 0.226 | RANDOM | 30.832 |
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] | |
0.66 | 0.79 | -1.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.601 |
r_dihedral_angle_3_deg | 15.703 |
r_dihedral_angle_4_deg | 13.716 |
r_dihedral_angle_1_deg | 8.983 |
r_scangle_it | 6.81 |
r_scbond_it | 4.783 |
r_mcangle_it | 3.225 |
r_mcbond_it | 2.387 |
r_angle_refined_deg | 1.194 |
r_symmetry_vdw_refined | 0.56 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2264 |
Nucleic Acid Atoms | |
Solvent Atoms | 204 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
AMoRE | phasing |