5F3K
X-Ray Crystallographic Structure of hTrap1 N-terminal Domain-apo
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5F5R |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 289 | 2 micro liter hTRAP1N, 25 mg/ml, in 30 mM TrisHCl pH 8.5, 0.15 M NaCl, and 1 mM TCEP was mixed with an equal volume of reservoir solution consisting of 100 mM HEPES pH 7.5, 100 mM CaCl2 , 23 percent PEG3350, 4 percent isopropanol, and 0.4 micro liter of 1 M LiCl2. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.25 | α = 90 |
b = 65.25 | β = 90 |
c = 233.372 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
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 | 93 | CCD | ADSC QUANTUM 315r | 2013-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97918 | APS | 19-ID |
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 | 1.82 | 77.79 | 99.4 | 0.053 | 14 | 6.7 | 52606 |
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 | 1.82 | 1.85 | 99.6 | 0.486 | 3.75 | 7 |
Refinement
Statistics | |||||||||||||||||||
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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 | FREE R-VALUE | 5F5R | 1.82 | 77.79 | 49944 | 2662 | 99.47 | 0.18332 | 0.18166 | 0.2145 | RANDOM | 29.583 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.75 | 0.38 | 0.75 | -1.13 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.569 |
r_dihedral_angle_4_deg | 18.468 |
r_dihedral_angle_3_deg | 14.691 |
r_scangle_it | 9.607 |
r_dihedral_angle_1_deg | 7.167 |
r_scbond_it | 6.144 |
r_mcangle_it | 3.851 |
r_mcbond_it | 2.489 |
r_angle_refined_deg | 0.835 |
r_chiral_restr | 0.075 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3162 |
Nucleic Acid Atoms | |
Solvent Atoms | 408 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |