3N5N
Crystal structure analysis of the catalytic domain and interdomain connector of human MutY homologue
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MUY | PDB Entry 1MUY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.9 | 298 | 20% PEG 3350, 0.2M Magnesium acetate, 0.005 M tris[2-carboxyethyl] phosphine (TCEP), 5% glycerol, 0.01 M spermidine, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.311 | α = 90 |
b = 82.167 | β = 100.9 |
c = 63.46 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 210 | Si(111) channel-cut monochromator, toroidal focusing mirror | 2007-04-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 1.65 | NSLS | X6A |
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 | 2.3 | 62.31 | 95.8 | 0.097 | 18.7 | 7.6 | 27002 | 25872 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.3 | 2.36 | 93.4 | 0.437 | 4.6 | 7.8 |
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 | SAD and Molecular Replacement | THROUGHOUT | PDB Entry 1MUY | 2.3 | 62.31 | 27002 | 24674 | 1302 | 95.66 | 0.20843 | 0.20616 | 0.25078 | RANDOM | 64.249 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
2.45 | -2.6 | -5.43 | 2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.257 |
r_dihedral_angle_3_deg | 15.363 |
r_dihedral_angle_4_deg | 15.092 |
r_scangle_it | 9.115 |
r_scbond_it | 6.328 |
r_dihedral_angle_1_deg | 5.891 |
r_mcangle_it | 3.835 |
r_mcbond_it | 2.459 |
r_angle_refined_deg | 1.991 |
r_chiral_restr | 0.159 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4037 |
Nucleic Acid Atoms | |
Solvent Atoms | 55 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MLPHARE | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |