1GL2
Crystal structure of an endosomal SNARE core complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1SFC | PDB ENTRY 1SFC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.2 | PROTEIN SOLUTION: 20 MG/ML OF QUATERNARY COMPLEX IN 20MM TRIS-HCL AT PH 7.4 WELL SOLUTION: 0.1M NA-ACETATE AT PH 5.2, 2.5 M NA-FORMIAT, 15% GLYCEROL HANGING DROPS WITH 2MUL + 2 MUL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
30 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.7 | α = 90 |
b = 41.1 | β = 109.4 |
c = 51.5 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | 100 | IMAGE PLATE | MAR scanner 345 mm plate | COSMIC MIRRORS CMF12-38CU6 | 2001-05-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | SIEMENS M18X |
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 | 1.9 | 15 | 93.7 | 0.0345 | 30.57 | 5.5 | 71259 | 14.3 |
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 | 1.9 | 2 | 88.8 | 0.137 | 11.35 | 4.6 |
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 | THROUGHOUT | PDB ENTRY 1SFC | 1.9 | 14.9 | 14797 | 737 | 92.7 | 0.176 | 0.176 | 0.224 | RANDOM | 22.1 |
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] | |
7.34 | 1.15 | -2.53 | -4.81 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 13.8 |
c_scangle_it | 3.98 |
c_mcangle_it | 2.58 |
c_scbond_it | 1.71 |
c_mcbond_it | 1.12 |
c_angle_deg | 0.8 |
c_improper_angle_d | 0.58 |
c_bond_d | 0.004 |
c_bond_d_na | |
c_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1796 |
Nucleic Acid Atoms | |
Solvent Atoms | 234 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
EPMR | phasing |