3RC0
Human SETD6 in complex with RelA Lys310 peptide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3QXY | PDB ENTRY 3QXY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 4.6 | 289 | 15% (w/v) polyethylene glycol (PEG) 3350, 0.1 M di-ammonium hydrogen citrate, pH 4.6, VAPOR DIFFUSION, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.79 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 61.621 | α = 78.73 |
b = 64.501 | β = 70.6 |
c = 73.759 | γ = 64.21 |
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 | CCD | MARMOSAIC 300 mm CCD | 2010-06-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 0.97918 | APS | 22-ID |
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 | 2.19 | 34.72 | 98.4 | 0.122 | 11.4 | 3.6 | 48552 | -3 | 22.27 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.19 | 2.27 | 97.4 | 0.427 | 2.4 | 3.2 | 4776 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MIR | THROUGHOUT | PDB ENTRY 3QXY | 2.19 | 34.72 | 0.04 | 46006 | 1923 | 92.53 | 0.1688 | 0.1661 | 0.2343 | RANDOM |
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] | |
-8.9117 | 0.9514 | -2.3711 | 4.7731 | -6.8429 | 4.1386 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.817 |
f_angle_d | 0.95 |
f_chiral_restr | 0.061 |
f_bond_d | 0.006 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6563 |
Nucleic Acid Atoms | |
Solvent Atoms | 485 |
Heterogen Atoms | 118 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SGXPRO | model building |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SGXPRO | phasing |