3TT9
Crystal structure of the stable degradation fragment of human plakophilin 2 isoform a (PKP2a) C752R variant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XM9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 293.15 | reservoir: 22% (w/v) PEG 3350, 75 M malonic acid pH 7.0, protein: 5 mg/mL in 20 mM HEPES, NaOH pH 7.5, 0.1 M NaCl, 3 mM DTT, mix 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.35 | α = 90 |
b = 63.038 | β = 90 |
c = 74.953 | 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 | RAYONIX MX-225 | 2009-05-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91841 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.55 | 35 | 99.4 | 32554 | 32363 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.55 | 1.59 | 98.3 | 2.87 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1XM9 | 1.55 | 33.42 | -3 | 32554 | 30744 | 1619 | 100 | 0.15994 | 0.15994 | 0.15822 | 0.15 | 0.19231 | 0.19 | RANDOM | 13.662 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
-0.47 | -0.31 | 0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.115 |
r_dihedral_angle_4_deg | 17.898 |
r_dihedral_angle_3_deg | 12.853 |
r_dihedral_angle_1_deg | 4.922 |
r_scangle_it | 4.466 |
r_scbond_it | 2.754 |
r_angle_refined_deg | 1.595 |
r_mcangle_it | 1.585 |
r_mcbond_it | 0.922 |
r_chiral_restr | 0.127 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1831 |
Nucleic Acid Atoms | |
Solvent Atoms | 282 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
PHASER | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |