5VAB
Crystal structure of ATXR5 PHD domain in complex with histone H3
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4QF3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 0.1M Hepes (pH 6.5), 10% PEG 6000 and 5% (+/-)-2-methyl-2,4-pentanediol. SET : 50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.31 | 46.72 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.01 | α = 90 |
b = 44.01 | β = 90 |
c = 71.948 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | IMAGE PLATE | RIGAKU RAXIS IV | 2015-01-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-D | 1.13 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.7 | 30 | 99.5 | 0.043 | 71.92 | 25.59 | 8225 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 4QF3 | 1.702 | 23.536 | 1.34 | 8223 | 433 | 99.65 | 0.1504 | 0.1489 | 0.1786 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.856 |
f_angle_d | 1.02 |
f_chiral_restr | 0.072 |
f_plane_restr | 0.007 |
f_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 486 |
Nucleic Acid Atoms | |
Solvent Atoms | 49 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |