8S1R
Crystal structure of SHANK1 PDZ in complex with a SLiM internal ligand
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6YWZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 293 | 20 % v/v ethylene glycol, 10 % w/v PEG 8000, 0.018 M magnesium chloride, 0.018 M calcium chloride, 0.1 M tris pH 7.5, 0.1 M bicine pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.01 | 69.31 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 149.101 | α = 90 |
b = 149.101 | β = 90 |
c = 64.066 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | PIXEL | DECTRIS EIGER2 X CdTe 9M | 2022-07-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9999 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim 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 | 1.979 | 129.125 | 100 | 0.123 | 0.039 | 0.999 | 14.7 | 20.7 | 57199 | 34.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.979 | 2.01 | 1.661 | 0.56 | 0.837 | 1.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.979 | 129.125 | 57178 | 3012 | 100 | 0.217 | 0.2158 | 0.2358 | 46.681 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.787 | 0.393 | 0.787 | -2.553 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.745 |
r_dihedral_angle_3_deg | 13.313 |
r_dihedral_angle_4_deg | 12.086 |
r_lrange_other | 8.826 |
r_lrange_it | 8.822 |
r_dihedral_angle_1_deg | 6.681 |
r_scangle_it | 6.273 |
r_scangle_other | 6.273 |
r_mcangle_it | 5.179 |
r_mcangle_other | 5.178 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3596 |
Nucleic Acid Atoms | |
Solvent Atoms | 115 |
Heterogen Atoms | 12 |
Software
Software | |
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Software Name | Purpose |
DIALS | data reduction |
PHASER | phasing |
Coot | model building |
REFMAC | refinement |