2IW5
Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 293 | VAPOR DIFFUSION, SITTING DROP, 20 DEGREES. DROP: 0.8 MICRO-LITERS OF PROTEIN (10 MG/ML IN 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, 5 MM DTT) PLUS 0.8 MICRO-LITERS OF CRYSTALLIZATION SOLUTION (0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, 10 MM DTT). RESERVOIR: 1 ML OF CRYSTALLIZATION SOLUTION. CRYSTALS APPEARED WITHIN 12 HOURS AND GREW TO THEIR FINAL SIZE WITHIN 10 DAYS. CRYO-PROTECTION SOLUTION: RESERVOIR SOLUTION PLUS 23 PERCENT (V/V) GLYCEROL. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
6.2 | 80.1 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 120.354 | ¦Á = 90 |
b = 178.222 | ¦Â = 90 |
c = 234.932 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 2 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 | CUSTOM | 2006-03-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | APS | 19-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 | 2.57 | 49.87 | 93.3 | 0.06 | 39.3 | 9.3 | 75117 | -3 | 70.3 |
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 | 2.57 | 2.61 | 60.6 | 0.64 | 2 | 6.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 2.57 | 20 | 73416 | 1498 | 93.2 | 0.204 | 0.203 | 0.212 | RANDOM | 67.13 |
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] | |
3.11 | -2.12 | -0.99 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.224 |
r_dihedral_angle_4_deg | 17.335 |
r_dihedral_angle_3_deg | 16.993 |
r_dihedral_angle_1_deg | 3.861 |
r_scangle_it | 2.211 |
r_angle_refined_deg | 1.448 |
r_scbond_it | 1.35 |
r_mcangle_it | 1.009 |
r_mcbond_it | 0.599 |
r_nbtor_refined | 0.308 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6293 |
Nucleic Acid Atoms | |
Solvent Atoms | 78 |
Heterogen Atoms | 69 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
SHELX | phasing |