7QQF
Crystal structure of unliganded MYORG
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2F2H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 291 | 100 mM HEPES pH 7.0, 10% PEG MME5000 and 5% tasimate pH 7.0. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.16 | 61.13 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.109 | α = 88.062 |
b = 78.986 | β = 78.801 |
c = 180.113 | γ = 62.714 |
Symmetry | |
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Space Group | P 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 XE 16M | 2019-06-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97951 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.43 | 66.57 | 98.2 | 0.066 | 0.093 | 0.066 | 0.983 | 8.2 | 2.2 | 131515 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.43 | 2.47 | 1.071 | 1.514 | 1.071 | 0.515 | 1 | 2.1 |
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 | THROUGHOUT | 2F2H | 2.43 | 66.57 | 131476 | 6445 | 98.149 | 0.212 | 0.2108 | 0.233 | 58.353 |
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] | |
-0.158 | 0.096 | -1.604 | 1.904 | 0.501 | -3.268 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.627 |
r_dihedral_angle_4_deg | 17.561 |
r_dihedral_angle_3_deg | 16.065 |
r_dihedral_angle_1_deg | 7.035 |
r_lrange_it | 3.972 |
r_lrange_other | 3.966 |
r_scangle_it | 1.54 |
r_scangle_other | 1.54 |
r_mcangle_it | 1.53 |
r_mcangle_other | 1.53 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19386 |
Nucleic Acid Atoms | |
Solvent Atoms | 319 |
Heterogen Atoms | 531 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
Aimless | data scaling |
PHASER | phasing |