3C8P
X-ray structure of Viscotoxin A1 from Viscum album L.
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 7.5 | 298 | 1.4M Sodium citrate, 0.1 M HEPES pH 7.5, vapor diffusion, temperature 298K, pH 7.50 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.6 | 52.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.73 | α = 90 |
b = 65.73 | β = 90 |
c = 47.16 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
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 | BRUKER SMART 6000 | OSMIC FOCUSSING MIRRORS | 2004-10-10 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | IMAGE PLATE | MAR scanner 345 mm plate | 2005-02-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | BRUKER AXS MICROSTAR | |||
2 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE BW7B | EMBL/DESY, Hamburg | BW7B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | |||||||
1,2 | 1.25 | 47.16 | 100 | 0.0891 | 0.031 | 25.5 | 1.8 | 29217 | 11.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.25 | 1.35 | 100 | 0.3038 | 0.3038 | 2.61 | 1.75 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | SAD | FREE R | 1.25 | 47.16 | 29166 | 1445 | 100 | 0.1498 | 0.151 | 0.191 | RANDOM | 17.81 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
1 | 801.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.36 |
s_approx_iso_adps | 0.108 |
s_zero_chiral_vol | 0.072 |
s_non_zero_chiral_vol | 0.065 |
s_similar_adp_cmpnt | 0.038 |
s_angle_d | 0.028 |
s_bond_d | 0.013 |
s_anti_bump_dis_restr | 0.013 |
s_rigid_bond_adp_cmpnt | 0.004 |
s_similar_dist |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 674 |
Nucleic Acid Atoms | |
Solvent Atoms | 135 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
SHELX | refinement |
PDB_EXTRACT | data extraction |
SAINT | data reduction |
SADABS | data scaling |
XPREP | data reduction |
SHELXD | phasing |
SHELXE | model building |
SHELXL-97 | refinement |