7SOH
Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6ATW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 298 | 0.2 M tri-Potassium Citrate, 20% (w/v) PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.67 | 26.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 22.498 | α = 90 |
b = 26.35 | β = 90 |
c = 47.738 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | CCD | RIGAKU SATURN 944+ | 2016-10-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.81 | 50 | 86 | 0.057 | 0.064 | 0.988 | 33 | 5.4 | 2451 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.81 | 1.875 | 15.6 | 0.95 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 6ATW | 1.81 | 23.87 | 2339 | 114 | 85.68 | 0.175 | 0.1734 | 0.212 | RANDOM | 13.514 |
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] | |
-0.64 | 0.9 | -0.27 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.11 |
r_dihedral_angle_4_deg | 27.127 |
r_dihedral_angle_3_deg | 14.708 |
r_dihedral_angle_1_deg | 7.129 |
r_angle_refined_deg | 1.855 |
r_angle_other_deg | 1.166 |
r_chiral_restr | 0.118 |
r_bond_refined_d | 0.018 |
r_bond_other_d | 0.008 |
r_gen_planes_refined | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 276 |
Nucleic Acid Atoms | |
Solvent Atoms | 15 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |