Structure of Domain of Unknown Function 507 (DUF507) in Space Group P3(2)21
X-RAY DIFFRACTION - SOLUTION SCATTERING
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 8T8K | |
Solution Scattering Data Acquistion | 1 |
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Scattering Type | x-ray |
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Radiation/Neutron Source | Advanced Light Source |
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Synchrotron | |
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Beamline Type | 12.3.1 |
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Detector Type | |
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Detector Manufacturer Details | Pilatus detector |
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Temperature (K) | 293 |
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pH | |
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Numer of Time Frames Used | |
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Protein Concentration Range (mg/mL) | |
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Sample Buffer | |
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Data Reduction Software | |
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Guiner Mean Radius Of Gyration (nm) | 22.7 |
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Sigma Mean Radius Of Gyration | 0.2 |
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R(XS-1) Mean Cross Sectional Radii (nm) | |
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R(XS-1) Sigma Mean Cross Sectional Radii | |
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R(XS-2) Mean Cross Sectional Radii (nm) | |
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R(XS-2) Sigma Mean Cross Sectional Radii | |
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P(R) Protein Length (nm) | |
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Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | | 286 | 0.1 M MES monohydrate pH 6.5 and 12% w/v PEG 20,000 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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3.13 | 60.64 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 83.096 | α = 90 |
b = 83.096 | β = 90 |
c = 68.796 | γ = 120 |
Symmetry |
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Space Group | P 32 2 1 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 100 | CMOS | RDI CMOS_8M | | 2022-04-29 | M | SINGLE WAVELENGTH |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 1.0722 | ALS | 4.2.2 |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 |
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1 | 1.9 | 41.55 | 99.8 | 0.079 | | 0.084 | 0.026 | 0.999 | | 18.6 | 10 | | 21999 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 1.9 | 1.94 | 98.5 | 1.611 | | 1.741 | 0.643 | 0.575 | | | 6.9 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.9 | 41.55 | | 0.19 | | 21999 | 2022 | 99.78 | | 0.2062 | 0.2053 | 0.2245 | | |
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] |
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| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 12.494 |
f_angle_d | 0.634 |
f_chiral_restr | 0.042 |
f_plane_restr | 0.005 |
f_bond_d | 0.004 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1487 |
Nucleic Acid Atoms | |
Solvent Atoms | 55 |
Heterogen Atoms | 15 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
Aimless | data scaling |
XDS | data reduction |
PHASER | phasing |