5DO6
Crystal structure of Dendroaspis polylepis venom mambalgin-1 T23A mutant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.6 | 293 | Protein: redissolved from lyophilized at 5mg/ml mamb-1-T23A in 50mM Na Acetate, pH 5.5. Precipitant: 21.6% PEG600, 3.6% PEG 20K 0.18M mixed L-malic acid, MES, Tris (pH4) and mixed sodium Malonate, imidazole, boric acid(pH10) in the ratio 40:60. Cryoprotectant: 30% MPEG 550, 40% CryoProtX cryomix9, 10% NaAc pH 6.5, 0.1M potassium iodide soaked for 1 min. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.34 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.9 | α = 90 |
b = 100.99 | β = 90 |
c = 53.48 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 315 | X-ray centering - Helical scan | 2015-06-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 0.9801 | SOLEIL | PROXIMA 2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.697 | 37 | 97.5 | 0.061 | 0.057 | 21.83 | 7.1 | 16719 | 31543 | -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 | 1.697 | 1.74 | 78.7 | 0.408 | 4.64 | 4.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | SAD | THROUGHOUT | 1.697 | 27.95 | 1.38 | 16719 | 837 | 97.69 | 0.1731 | 0.1715 | 0.2048 | Random |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.35 |
f_angle_d | 1.017 |
f_chiral_restr | 0.043 |
f_bond_d | 0.006 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 898 |
Nucleic Acid Atoms | |
Solvent Atoms | 165 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | phasing |
Coot | model building |