1XDT
COMPLEX OF DIPHTHERIA TOXIN AND HEPARIN-BINDING EPIDERMAL GROWTH FACTOR
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MDT | PDB ENTRY 1MDT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.5 | PROTEIN (15 MG/ML) IN 10 MM TRIS-HCL (PH 7.5), 0.15 M NACL MIXED WITH AN EQUAL VOLUME OF PRECIPITANT CONTAINING 50 MM TRIS-HCL (PH 7.5), 0.15 M NACL, 5% (V/V) GLYCEROL, 22-30% (W/V) POLYETHYLENE GLYCOL 3350; AND EQUILIBRATED BY VAPOR DIFFUSION AGAINST PRECIPITANT, vapor diffusion |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.4 | α = 90 |
b = 103.7 | β = 90 |
c = 127.7 | 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 | IMAGE PLATE | MACSCIENCE | MIRRORS | 1996-10-09 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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 | 2.65 | 25 | 88.5 | 0.052 | 0.052 | 27.9 | 3.6 | 54532 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.65 | 2.74 | 79.2 | 0.152 | 0.152 | 5 | 2.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1MDT | 2.65 | 25 | 15511 | 750 | 88.5 | 0.172 | 0.172 | 0.29 | RANDOM | 37.9 |
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 |
x_dihedral_angle_d | 24.3 |
x_scangle_it | 7.35 |
x_scbond_it | 5.23 |
x_mcangle_it | 5.21 |
x_mcbond_it | 3.45 |
x_angle_deg | 1.5 |
x_improper_angle_d | 1.34 |
x_bond_d | 0.009 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4306 |
Nucleic Acid Atoms | |
Solvent Atoms | 48 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
X-PLOR | refinement |