5WW0
Crystal structure of Set7, a novel histone methyltransferase in Schizossacharomyces pombe
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3KMA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 286 | 30% ethylene glycol (cryoprotectant for 101)250mM Ammonium Sulfate, 14% PEG 3.350, 1(protein):1(buffer):0.4 ratio of 0.3M Glycyl-glycyl-glycine (~48mM final conc), Protein concentration(4mg/mL), Protein buffer(10mM Tris pH 7.5) Temperature(13), Well volume(500ul), 5uL of HCL (12.1M) was added to the reservoir drop prior to drop setup |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 41.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.119 | α = 90 |
b = 66.119 | β = 90 |
c = 259.073 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 2 |
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 | ADSC QUANTUM 270 | 2016-05-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 7A (6B, 6C1) | 0.97933 | PAL/PLS | 7A (6B, 6C1) |
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 | 2.1 | 50 | 95 | 0.087 | 4 | 10.6 | 19879 |
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 | 2.1 | 2.14 | 93 | 0.824 | 10.8 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3KMA | 2.1 | 45 | 18019 | 960 | 92.3 | 0.179 | 0.176 | 0.239 | RANDOM | 30.49 |
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] | |
-0.14 | -0.07 | -0.14 | 0.45 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.057 |
r_dihedral_angle_3_deg | 14.498 |
r_dihedral_angle_4_deg | 12.454 |
r_long_range_B_refined | 8.547 |
r_long_range_B_other | 8.422 |
r_dihedral_angle_1_deg | 7.037 |
r_scangle_other | 6.039 |
r_mcangle_it | 4.139 |
r_mcangle_other | 4.137 |
r_scbond_it | 3.833 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2013 |
Nucleic Acid Atoms | |
Solvent Atoms | 199 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Sir2014 | phasing |
PHENIX | model building |