3ODV
X-ray structure of kaliotoxin by racemic protein crystallography
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 292 | 1.8 M sodium citrate tribasic dihydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.74 | 29.41 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 25.15 | α = 109.39 |
b = 30.511 | β = 97.39 |
c = 41.097 | γ = 97.09 |
Symmetry | |
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Space Group | P -1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | 2007-12-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 0.95373 | APS | 23-ID-B |
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 | 0.95 | 50 | 88.2 | 0.057 | 19.9 | 4.3 | 62285 | 62285 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 0.95 | 0.98 | 50.9 | 1.8 | 3.5 | 3600 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | AB INITIO PHASING | THROUGHOUT | 0.95 | 38.13 | 59134 | 3130 | 87.92 | 0.18878 | 0.188 | 0.20326 | RANDOM | 10.564 |
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] | |
0.22 | 0.12 | -0.21 | -0.53 | 0.1 | 0.35 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.988 |
r_dihedral_angle_4_deg | 14.498 |
r_dihedral_angle_3_deg | 13.919 |
r_dihedral_angle_1_deg | 5.446 |
r_scangle_it | 5.161 |
r_scbond_it | 3.483 |
r_mcangle_it | 2.561 |
r_angle_refined_deg | 1.646 |
r_mcbond_it | 1.632 |
r_rigid_bond_restr | 1.232 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 566 |
Nucleic Acid Atoms | |
Solvent Atoms | 90 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
SHELXD | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |