3LLR
Crystal structure of the PWWP domain of Human DNA (cytosine-5-)-methyltransferase 3 alpha
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KHC |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | 28% PEG 3,350, 0.1 M ammonium sulfate, 0.1M BisTris, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.5 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 67.11 | ¦Á = 90 |
b = 83.99 | ¦Â = 90.48 |
c = 74.59 | ¦Ã = 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 | MARMOSAIC 225 mm CCD | 2009-09-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.9792 | CLSI | 08ID-1 |
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 | 60 | 99 | 0.0747 | 12.35 | 3.76 | 36937 | 36565 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1 | 2.3 | 2.4 | 98.5 | 0.2559 | 4.16 | 3.77 | 4407 |
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 | 1KHC | 2.3 | 50.1 | 34711 | 1819 | 100 | 0.21811 | 0.2161 | 0.25597 | RANDOM | 15.912 |
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] | |
-0.01 | 0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 23.738 |
r_dihedral_angle_3_deg | 13.224 |
r_dihedral_angle_4_deg | 12.239 |
r_dihedral_angle_1_deg | 4.897 |
r_scangle_it | 1.169 |
r_angle_refined_deg | 0.954 |
r_mcangle_it | 0.706 |
r_scbond_it | 0.681 |
r_mcbond_it | 0.379 |
r_chiral_restr | 0.071 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5340 |
Nucleic Acid Atoms | |
Solvent Atoms | 362 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
MxDC | data collection |
BALBES | phasing |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |