4I6O
Crystal structure of chemically synthesized human anaphylatoxin C3a
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 277 | VAPOR DIFFUSION, HANGING DROP, 1 uL 5 mg/mL lyophilized C3a in 2 mM hydrochloric acid + 1 uL reservoir (0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic, 49-51% v/v MPD, pH 8.5) against 500 uL reservoir, prepared at 277K, incubated at 281K for 96 hours, stored at 277K, rhomboid-shaped crystals appeared after 6 days and grew to a final size of 0.5 x 0.2 x 0.2 mm |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.285 | α = 90 |
b = 68.285 | β = 90 |
c = 39.266 | γ = 120 |
Symmetry | |
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Space Group | P 63 |
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 | 2012-10-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.95370 | Australian Synchrotron | MX2 |
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 | 2.14 | 39.27 | 100 | 0.106 | 15.9 | 22.1 | 5870 | 2 | 61.793 |
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 | 2.14 | 2.2 | 100 | 0.787 | 3.4 | 22 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2.14 | 19.42 | 2 | 5870 | 4899 | 946 | 99.81 | 0.21839 | 0.21839 | 0.20845 | 0.26793 | RANDOM | 61.793 |
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] | |
-0.04 | -0.04 | -0.04 | 0.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.643 |
r_dihedral_angle_3_deg | 20.819 |
r_dihedral_angle_4_deg | 18.554 |
r_dihedral_angle_1_deg | 4.943 |
r_angle_refined_deg | 1.907 |
r_angle_other_deg | 0.895 |
r_chiral_restr | 0.111 |
r_bond_refined_d | 0.017 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 557 |
Nucleic Acid Atoms | |
Solvent Atoms | 19 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |