3K3N
Crystal structure of the catalytic core domain of human PHF8
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2YU2 | PDB ENTRY 2YU2 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 6.5 | 298 | 200mM KCl, 100mM Mes, 20% PEG5K, pH 6.5, VAPOR DIFFUSION, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.55 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.238 | α = 90 |
b = 52.583 | β = 90 |
c = 134.93 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 200 | CCD | MARMOSAIC 225 mm CCD | 2009-05-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.97939 | SSRF | BL17U |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.4 | 50 | 98 | 0.055 | 0.06 | 31 | 5.7 | 15300 | 14988 | 3 | 3 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.4 | 2.44 | 4.1 | 0.426 | 0.37 | 2.6 | 3.7 | 616 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2YU2 | 2.4 | 20 | 14861 | 14109 | 752 | 98.32 | 0.224 | 0.222 | 0.261 | RANDOM | 33.634 |
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] | |
2.17 | -0.41 | -1.76 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.369 |
r_dihedral_angle_4_deg | 17.318 |
r_dihedral_angle_3_deg | 15.909 |
r_dihedral_angle_1_deg | 5.328 |
r_scangle_it | 1.318 |
r_angle_refined_deg | 1.019 |
r_scbond_it | 0.807 |
r_mcangle_it | 0.617 |
r_mcbond_it | 0.329 |
r_chiral_restr | 0.07 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2648 |
Nucleic Acid Atoms | |
Solvent Atoms | 111 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
MAR345 | data collection |
PHASER | phasing |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |