4PET
CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM COLWELLIA PSYCHRERYTHRAEA (CPS_0129, TARGET EFI-510097) WITH BOUND CALCIUM AND PYRUVATE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 298 | Protein (74.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 1 mM D-Glycerate); Reservoir (0.1 M HEPES pH 7.0, 30 %(v/v) Jeffamine ED-2001 pH 7.0); Cryoprotection (80% Reservoir, 20% Ethylene glycol) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.82 | 32.57 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.827 | α = 90 |
b = 70.249 | β = 90 |
c = 154.927 | 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 MX225HE | MIRRORS | 2014-04-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 31-ID | 0.9793 | APS | 31-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 1.9 | 77.46 | 99.2 | 0.098 | 0.027 | 27.1 | 13.8 | 48462 | 27.04 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.9 | 1.94 | 90.4 | 0.926 | 0.299 | 2.3 | 9.6 | 2786 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | FREE R-VALUE | 1.9 | 34.255 | 1.33 | 91454 | 4612 | 98.61 | 0.1563 | 0.1536 | 0.2072 | Random Selection | 31.39 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.99 |
f_angle_d | 1.286 |
f_chiral_restr | 0.075 |
f_bond_d | 0.014 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5242 |
Nucleic Acid Atoms | |
Solvent Atoms | 477 |
Heterogen Atoms | 21 |
Software
Software | |
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Software Name | Purpose |
PDB_EXTRACT | data extraction |
PHENIX | refinement |
Aimless | data scaling |