4PZI
Zinc finger region of MLL2 in complex with CpG DNA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.5 | 291 | 25% PEG-3350, 0.2 M ammonium sulfate, 0.1 M TRIS, pH 8.5, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.8 | 55.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.736 | α = 90 |
b = 41.005 | β = 99.24 |
c = 55.508 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 315 | 2013-08-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97918 | 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 | 2.15 | 35.36 | 99.8 | 0.066 | 14.3 | 3.7 | 8659 |
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 | 2.15 | 2.22 | 100 | 1.13 | 1.4 | 3.7 | 729 |
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 | structure of isomorphous crystal was solved by molecular replacement using currently unpublished models of same protein and DNA, respectively. | 2.15 | 34.91 | 8658 | 398 | 99.72 | 0.228 | 0.2258 | 0.2728 | RANDOM | 61.8311 |
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] | |
-0.74 | 0.68 | -2.17 | 2.55 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.206 |
r_dihedral_angle_3_deg | 14.005 |
r_dihedral_angle_4_deg | 12.299 |
r_dihedral_angle_1_deg | 5.77 |
r_mcangle_it | 3.962 |
r_mcbond_it | 2.794 |
r_mcbond_other | 2.779 |
r_angle_refined_deg | 1.434 |
r_angle_other_deg | 1.261 |
r_chiral_restr | 0.081 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 441 |
Nucleic Acid Atoms | 486 |
Solvent Atoms | 8 |
Heterogen Atoms | 3 |
Software
Software | |
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Software Name | Purpose |
Aimless | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |