3UJ3
Crystal Structure of the synaptic tetramer of the G-Segment Invertase (Gin)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1ZR4 | Gin Homology Model of subunit A of 1ZR4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 289 | 10% Ammonium Sulfate, 20% Ethylene Glycol, 10 mM MgSO4, 100 mM MES 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.33 | 76.91 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 116.84 | α = 90 |
b = 116.84 | β = 90 |
c = 117.64 | γ = 120 |
Symmetry | |
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Space Group | P 62 2 2 |
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 | ADSC QUANTUM 315r | 2006-08-06 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210r | 2006-05-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-C | 0.97918 | APS | 24-ID-C |
2 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 1.07210 | ALS | 8.2.2 |
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 | |||||||||
1,2 | 3.5 | 30 | 99 | 8.59 | 5.7 | 6206 | 6313 | 3 | 3 |
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 | SIRAS | THROUGHOUT | Gin Homology Model of subunit A of 1ZR4 | 3.51 | 46.48 | 5824 | 375 | 97.92 | 0.25894 | 0.2568 | 0.28918 | RANDOM | 146.395 |
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] | |
-13.08 | -6.54 | -13.08 | 19.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_bonded | 82.521 |
r_dihedral_angle_2_deg | 33.388 |
r_dihedral_angle_3_deg | 22.316 |
r_dihedral_angle_4_deg | 13.221 |
r_dihedral_angle_1_deg | 5.107 |
r_rigid_bond_restr | 1.408 |
r_angle_refined_deg | 0.988 |
r_chiral_restr | 0.075 |
r_bond_refined_d | 0.006 |
r_gen_planes_refined | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 984 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SOLVE | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |