4NIB
Crystal structure of human insulin mutant B20 D-ala, B23 D-ala
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1B2A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 294 | These insulin crystals were obtained from a co-crystallization experiment with insulin receptor fragment IR310.T. Crystals were formed in the presence of IR310.T as detailed for the IR310.T complex with native human insulin - in Menting et al. 2013, Nature 493:241-245. Crystallant was 0.7 M trisodium citrate, 0.1 M imidazole-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.39 | 63.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.03 | α = 90 |
b = 78.03 | β = 90 |
c = 78.03 | γ = 90 |
Symmetry | |
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Space Group | I 21 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 315r | 2013-04-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
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 | 1.3 | 20 | 99.8 | 11.5 | 19350 | 0.66 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 1.3 | 1.35 | 89.1 | 0.55 | 7.2 | 1852 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1B2A | 1.4 | 18.392 | 0.53 | 1.34 | 15723 | 1568 | 99.94 | 0.1433 | 0.1411 | 0.163 | random |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.858 |
f_angle_d | 1.073 |
f_chiral_restr | 0.076 |
f_bond_d | 0.009 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 407 |
Nucleic Acid Atoms | |
Solvent Atoms | 83 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |