4LZG
Binary complex of human DNA Polymerase Mu with DNA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2IHM | hPol Mu Loop2 truncation variant in ternary complex with single-nucleotide gapped DNA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 277 | Crystals were grown by mixing 1uL of the protein/DNA complex with 1uL of mother liquor (85mM MES pH 6.5, 85mMCaCl2, 42.5mM NaCl, 8.5% PEG3350, 11% glycerol), using the sitting drop vapor diffusion technique. Crystals were transferred to a cryoprotectant solution containing 0.1M MES pH 6.5, 0.1M CaCl2, 50mM NaCl, 10mM MgCl2, 20% PEG3350, 15% glycerol in three steps. , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 50.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.003 | α = 90 |
b = 68.514 | β = 90 |
c = 110.307 | 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 | 93 | CCD | MARMOSAIC 300 mm CCD | 2012-10-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 22-ID | 1.0 | APS | 22-ID |
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 | 1.599 | 50 | 98.6 | 0.062 | 13.8 | 6.2 | 60033 | 60033 | -3 | 17.45 |
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 | 1.599 | 1.63 | 83.1 | 0.272 | 2.4 | 2520 |
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 (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | hPol Mu Loop2 truncation variant in ternary complex with single-nucleotide gapped DNA | 1.599 | 34.932 | 1.34 | 60033 | 59953 | 2991 | 98.51 | 0.18 | 0.175 | 0.1742 | 0.2046 | random | 14.6934 |
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 | 13.129 |
f_angle_d | 1.448 |
f_chiral_restr | 0.095 |
f_bond_d | 0.011 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2551 |
Nucleic Acid Atoms | 344 |
Solvent Atoms | 513 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
HKL-2000 | data reduction |