5VTK
Structure of Pin1 WW Domain Variant 1 with beta3-Ser Loop Substitution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 298 | 0.1 M HEPES, pH 7.5, 4.3 M sodium chloride (Hampton CSII #36), crystal grew after ~6 months, treated with 4:1 (CS2 #36):glycerol prior to freezing in cryostream |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 49.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.629 | α = 90 |
b = 47.629 | β = 90 |
c = 60.741 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2014-08-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | BRUKER IMUS MICROFOCUS | 0.72 |
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 | 1.99 | 34.12 | 99.7 | 0.102 | 38.41 | 40.8 | 3112 | 10.2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1 | 1.99 | 2.02 | 97.7 | 0.324 | 11.27 | 24.6 |
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 | PDB entry 5VTJ | 1.99 | 34.12 | 2804 | 287 | 99.87 | 0.1625 | 0.15685 | 0.22098 | RANDOM | 14.392 |
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] | |
-0.03 | -0.01 | -0.03 | 0.09 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.732 |
r_dihedral_angle_3_deg | 12.501 |
r_long_range_B_refined | 7.025 |
r_dihedral_angle_1_deg | 6.794 |
r_long_range_B_other | 6.542 |
r_dihedral_angle_4_deg | 6.347 |
r_scangle_other | 3.619 |
r_mcangle_it | 3.469 |
r_mcangle_other | 3.461 |
r_scbond_it | 2.158 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 281 |
Nucleic Acid Atoms | |
Solvent Atoms | 61 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XPREP | data reduction |
APEX 2 | data collection |
PHASER | phasing |
XPREP | data scaling |