9FB8
XChem refined PIF1-x0076 complex
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6HPH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277.15 | XChem 0.045uls compound (0.5M) in DMSO echo dispensed into crystal drop Drop = 0.3uls protein + 0.3us well +0.001uls seeds. Protein = 25uls 30mgs/ml human PIF1 (206-620) in 10mM Tris pH 7.5, 175mM NaCl, 2%glycerol, 5mM DTT, 0.1mM PMSF + 21uls 10mM Tris, 2.7uls 0.2M MgCl2, 5uls 100mM AMPPNP + 27uls H2O. Well = 4% Glycerol, 27% PEG 2KMME, 0.1M NaAcetate, 0.1M Tris pH8.5. Set up on douglas instruments robot - tray on ice - set-up room temperature - crystallised 4 degrees C. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.24 | 45.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.6 | α = 90 |
b = 143.714 | β = 90 |
c = 77.238 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 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 | PIXEL | DECTRIS PILATUS 6M-F | 2018-03-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91587 | Diamond | I04-1 |
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 | 1.727 | 27.83 | 99.6 | 0.999 | 19.5 | 6.5 | 43220 |
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 | 1.73 | 1.77 | 0.866 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 1.727 | 27.83 | 43195 | 2134 | 99.617 | 0.175 | 0.1734 | 0.2114 | 30.663 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
-2.208 | 0.903 | 1.304 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 16.622 |
r_dihedral_angle_3_deg | 13.335 |
r_dihedral_angle_2_deg | 9.591 |
r_lrange_it | 7.677 |
r_scangle_it | 6.015 |
r_dihedral_angle_1_deg | 5.641 |
r_scbond_it | 4.131 |
r_mcangle_it | 3.331 |
r_mcbond_it | 2.479 |
r_angle_refined_deg | 1.896 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3150 |
Nucleic Acid Atoms | |
Solvent Atoms | 373 |
Heterogen Atoms | 68 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
DIALS | data scaling |
REFMAC | phasing |