4MGP
Structure of racemic Ala-(8,13,18) Magainin 2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2MAG | PDB entry 2MAG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 298 | Precipitant solution contained 0.1 M sodium citrate tribasic, pH 5.6, and 35% v/v tert-butanol. No additional cryoprotectant was necessary for vitrification of crystals in LN2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.38 | α = 89.97 |
b = 53.459 | β = 90.07 |
c = 29.75 | γ = 89.98 |
Symmetry | |
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Space Group | I -4 2 d |
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 | MARMOSAIC 300 mm CCD | 2013-06-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.9786 | APS | 21-ID-G |
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 | 1.75 | 26.72 | 95.4 | 0.092 | 32.17 | 22.4 | 2247 | 26.4 |
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 | 1.75 | 1.79 | 64.3 | 0.374 | 3.9 | 4.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 2MAG | 1.75 | 26.69 | 2169 | 2169 | 95 | 95.42 | 0.1983 | 0.1965 | 0.2328 | RANDOM | 31.59 |
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] | |
-0.63 | -0.63 | 1.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.848 |
r_dihedral_angle_3_deg | 16.79 |
r_dihedral_angle_1_deg | 5.806 |
r_angle_refined_deg | 2.43 |
r_angle_other_deg | 1.189 |
r_chiral_restr | 0.165 |
r_bond_refined_d | 0.023 |
r_gen_planes_refined | 0.012 |
r_bond_other_d | 0.001 |
r_gen_planes_other | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 163 |
Nucleic Acid Atoms | |
Solvent Atoms | 5 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XPREP | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
EMBL | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |