3ZPO
Crystal structure of JmjC domain of human histone demethylase UTY with bound GSK J1
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ZLI | PDB ENTRY 3ZLI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 15%(W/V) PEG 3350, 0.1M MAGNESIUM FORMATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.28 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 91.158 | ¦Á = 90 |
b = 110.755 | ¦Â = 90 |
c = 119.492 | ¦Ã = 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 | 100 | PIXEL | DECTRIS PILATUS 2M | 2013-02-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | Diamond | I04-1 |
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 | 39.83 | 99.1 | 0.11 | 10.4 | 6.9 | 81514 | 2 |
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 | 2.04 | 97.1 | 0.77 | 2 | 6.1 |
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 | PDB ENTRY 3ZLI | 2 | 37.51 | 77371 | 4068 | 98.9 | 0.17906 | 0.17745 | 0.20977 | RANDOM | 30.8 |
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] | |
-2.03 | 0.62 | 1.4 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.262 |
r_dihedral_angle_4_deg | 17.769 |
r_dihedral_angle_3_deg | 13.055 |
r_dihedral_angle_1_deg | 5.81 |
r_mcangle_it | 2.043 |
r_scbond_it | 1.795 |
r_angle_refined_deg | 1.395 |
r_mcbond_it | 1.355 |
r_mcbond_other | 1.354 |
r_angle_other_deg | 0.956 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7033 |
Nucleic Acid Atoms | |
Solvent Atoms | 541 |
Heterogen Atoms | 130 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |