7MMY
Racemic structure of the cyclic plant peptide PDP-23
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7L51 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 293 | Crystals were obtained from a racemic mix of 7mg/ml each of L- and D-peptide in 0.2 M trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% PEG monomethyl ether 2000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.58 | 22.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 27.527 | α = 90 |
b = 49.008 | β = 92.284 |
c = 29.402 | γ = 90 |
Symmetry | |
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Space Group | P 1 21/n 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 | PIXEL | DECTRIS EIGER X 16M | 2020-10-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.9537 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | CC (Half) | 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 | 1.46 | 49.01 | 98.8 | 0.998 | 10.6 | 6.4 | 13346 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.46 | 1.49 | 80.8 | 0.833 | 2.5 | 6.1 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7L51 | 1.464 | 25.198 | 13041 | 619 | 98.691 | 0.192 | 0.1881 | 0.2763 | 20.907 |
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] | |
-1.867 | -0.719 | -2.209 | 4.12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.36 |
r_dihedral_angle_3_deg | 10.299 |
r_rigid_bond_restr | 8.917 |
r_dihedral_angle_1_deg | 8.137 |
r_scangle_it | 5.811 |
r_scangle_other | 5.669 |
r_lrange_other | 5.145 |
r_lrange_it | 5.129 |
r_scbond_it | 5.108 |
r_scbond_other | 4.999 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 438 |
Nucleic Acid Atoms | |
Solvent Atoms | 45 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |