4Z9B
Crystal structure of Low Molecular Weight Protein Tyrosine Phosphatase isoform A complexed with benzylphosphonic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5PNT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291 | 32% (w/v) PEG 5000, 0.1 M malic acid:Tris, molar ratio 1:2, pH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 32.088 | α = 90 |
b = 54.287 | β = 90 |
c = 97.468 | 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 | APEX II CCD | 2013-04-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | 1.5418 |
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 | 2.4 | 27.8 | 99.7 | 0.1455 | 16.34 | 11.84 | 7097 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.4 | 2.45 | 100 | 0.5618 | 2.94 | 11.58 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 5PNT | 2.41 | 27.8 | 6641 | 325 | 99.26 | 0.21875 | 0.21479 | 0.30148 | RANDOM | 35.003 |
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] | |
1.77 | -1.7 | -0.07 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.456 |
r_dihedral_angle_4_deg | 20.462 |
r_dihedral_angle_3_deg | 15.492 |
r_dihedral_angle_1_deg | 6.825 |
r_long_range_B_refined | 4.635 |
r_long_range_B_other | 4.634 |
r_mcangle_it | 2.513 |
r_mcangle_other | 2.512 |
r_scangle_other | 2.334 |
r_angle_refined_deg | 1.562 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1249 |
Nucleic Acid Atoms | |
Solvent Atoms | 69 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
APEX | data collection |
APEX | data reduction |
APEX | data scaling |
PHASER | phasing |
REFMAC | refinement |