3NFQ
Crystal structure of the conserved central domain of yeast Spn1/Iws1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 292 | potassium chloride, sodium thiocyanate, PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.08 | 40.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.6 | α = 90 |
b = 67.8 | β = 90 |
c = 76 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | M | MAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 0.9791, 0.9793, 0.9716 | ALS | 4.2.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.85 | 39.6 | 99.6 | 0.051 | 12.1 | 3.02 | 28618 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1.85 | 1.92 | 100 | 0.38 | 0.396 | 2.8 | 3.01 | 2813 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | MAD | THROUGHOUT | 1.85 | 33.15 | 28618 | 27160 | 1458 | 100 | 0.20658 | 0.20347 | 0.26456 | RANDOM | 34.686 |
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] | |
-1.12 | -0.43 | 1.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.773 |
r_dihedral_angle_4_deg | 22.922 |
r_dihedral_angle_3_deg | 15.771 |
r_scangle_it | 5.614 |
r_dihedral_angle_1_deg | 5.438 |
r_scbond_it | 3.515 |
r_mcangle_it | 2.288 |
r_angle_refined_deg | 1.71 |
r_mcbond_it | 1.431 |
r_nbtor_refined | 0.315 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2304 |
Nucleic Acid Atoms | |
Solvent Atoms | 414 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
CrystalClear | data collection |
SOLVE | phasing |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |