7MP2
CRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 IN COMPLEX WITH 1D-MYO-INOSITOL 1,5-BISDIPHOSPHATE TETRAKISPHOSPHATE (1,5-PP IP4)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7JTB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 281 | 0.1 M Bis-Tris propane, 35% 2-Ethoxyethanol, 0.001 mM Magnesium acetate, 5 mM 1D-MYO-INOSITOL 1,5-BISDIPHOSPHATE TETRAKISPHOSPHATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.94 | 68.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 168.9 | α = 90 |
b = 187.094 | β = 90 |
c = 90.385 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 PILATUS 6M | 2020-11-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.979460 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 3 | 50 | 99.7 | 0.204 | 0.999 | 12.71 | 13.3 | 58102 | 87.9 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3 | 3.18 | 98.7 | 3.623 | 0.596 | 0.69 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 7JTB | 3 | 49.16 | 53859 | 2775 | 97.4 | 0.2114 | 0.2097 | 0.2455 | RANDOM | 104.153 |
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] | |
2.21 | 5.58 | -7.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.599 |
r_dihedral_angle_4_deg | 15.163 |
r_dihedral_angle_3_deg | 15.021 |
r_dihedral_angle_1_deg | 7.621 |
r_angle_refined_deg | 1.243 |
r_angle_other_deg | 1.055 |
r_chiral_restr | 0.039 |
r_bond_refined_d | 0.004 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11504 |
Nucleic Acid Atoms | |
Solvent Atoms | 9 |
Heterogen Atoms | 264 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
XDS | data scaling |
REFMAC | phasing |