3RTO
Acoustically mounted porcine insulin microcrystals yield an X-ray SAD structure
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4INS | PDB ENTRY 4INS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | SMALL TUBES | 6 | Microcrystals are obtained by dissolving 0.025 g protein in 5 mL of crystallizing solution (200 mL 0.02 M HCl, 100 mL 0.20 M sodium citrate, 60 mL acetone, 20 mL water, 20 mL 0.12 M zinc sulfate) at 315K. The solution is then rapidly quenched to 293K by immersing it in a cool water bath. Quenching speed determines the resulting crystal size. 20-micron crystals are obtained by quenching in a 293K water bath, 10-micron crystals by quenching in a 283K water bath, and 5-micron crystals by quenching in ice water. pH 6.0, SMALL TUBES |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.88 | 34.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.7 | α = 90 |
b = 81.7 | β = 90 |
c = 33.8 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 4 | 2010-04-29 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 210 | 2010-07-30 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 315 | 2010-02-27 | M | SINGLE WAVELENGTH | ||||||
4 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2009-12-19 | M | SINGLE WAVELENGTH | ||||||
1,2,3,4 | 1 |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X12B | NSLS | X12B | |
2 | SYNCHROTRON | NSLS BEAMLINE X12C | NSLS | X12C | |
3 | SYNCHROTRON | NSLS BEAMLINE X25 | NSLS | X25 | |
4 | SYNCHROTRON | APS BEAMLINE 23-ID-D | APS | 23-ID-D |
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 | ||||||||
1,2,3,4 | 1.8 | 50 | 99.8 | 0.114 | 62.2 | 10.5 | 7783 | 7770 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | THROUGHOUT | PDB ENTRY 4INS | 1.8 | 40.85 | 7783 | 7413 | 357 | 99.83 | 0.18338 | 0.18135 | 0.22311 | RANDOM | 37.509 |
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] | |
0.18 | 0.09 | 0.18 | -0.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.003 |
r_dihedral_angle_3_deg | 17.954 |
r_dihedral_angle_4_deg | 8.064 |
r_dihedral_angle_1_deg | 6.773 |
r_scangle_it | 5.716 |
r_scbond_it | 3.423 |
r_angle_refined_deg | 2.784 |
r_mcangle_it | 2.626 |
r_mcbond_it | 1.37 |
r_chiral_restr | 0.134 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 806 |
Nucleic Acid Atoms | |
Solvent Atoms | 46 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
CBASS | data collection |
SHELXS | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |