4IYE
Crystal structure of AdTx1 (rho-Da1a) from eastern green mamba (Dendroaspis angusticeps)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FF4 | PDB ENTRY 1FF4 without loop 1 tip |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | Lyophilization | 8 | 273 | Crystallization during lyophilization due to increased concentration and low temperature. Cryoconditions: 27% PEG8K, 15% MPEG550, 10% glycerol, 0.09 M Tris-HCl, pH 8.0, Lyophilization, temperature 273K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.82 | 32.56 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.37 | α = 90 |
b = 37.37 | β = 90 |
c = 66.05 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
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 4 | mirrors | 2010-06-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-1 | 0.9334 | ESRF | ID14-1 |
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 | 1.95 | 32.36 | 93.9 | 0.171 | 0.16 | 11.43 | 8.44 | 4193 | 3937 | -4 | 25.325 |
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 | 1.95 | 2.07 | 69.1 | 1.088 | 0.947 | 1.12 | 2.89 | 660 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB ENTRY 1FF4 without loop 1 tip | 1.951 | 32.36 | -3 | 3937 | 3738 | 197 | 93.89 | 0.17545 | 0.17445 | 0.17033 | 0.25188 | RANDOM | 25.704 |
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] | |
1.63 | 1.63 | 1.63 | -5.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.032 |
r_dihedral_angle_3_deg | 14.462 |
r_sphericity_bonded | 12.756 |
r_dihedral_angle_4_deg | 9.449 |
r_dihedral_angle_1_deg | 7.225 |
r_rigid_bond_restr | 5.042 |
r_angle_refined_deg | 1.648 |
r_angle_other_deg | 1.233 |
r_chiral_restr | 0.08 |
r_bond_refined_d | 0.016 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 505 |
Nucleic Acid Atoms | |
Solvent Atoms | 70 |
Heterogen Atoms | 18 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
MOLREP | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |