4DKJ
CpG specific methyltransferase in complex with target DNA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 294 | 10% PEG 3350, 150 mM NaCl, 50 mM sodium. For cryoprotection glycerol was added to 25% v/v, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 83.95 | α = 90 |
b = 83.95 | β = 90 |
c = 173.84 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 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 | ADSC QUANTUM 315 | BENT MIRRORS | 2010-12-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | Diamond | I02 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.15 | 40 | 99.3 | 0.078 | 0.078 | 5.5 | 3.9 | 34324 | 34324 | 33.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.15 | 2.27 | 99.9 | 0.31 | 0.31 | 2.5 | 4 | 4957 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 2C7P | 2.15 | 38.6 | 34274 | 34274 | 1729 | 98.96 | 0.17832 | 0.17832 | 0.17632 | 0.21631 | RANDOM |
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 |
r_dihedral_angle_2_deg | 38.254 |
r_dihedral_angle_4_deg | 15.209 |
r_dihedral_angle_3_deg | 15.063 |
r_dihedral_angle_1_deg | 6.16 |
r_angle_other_deg | 3.966 |
r_angle_refined_deg | 1.253 |
r_symmetry_vdw_other | 0.38 |
r_nbd_other | 0.232 |
r_nbd_refined | 0.192 |
r_nbtor_refined | 0.181 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3199 |
Nucleic Acid Atoms | 570 |
Solvent Atoms | 267 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
MOLREP | phasing |
CHAINSAW | model building |
REFMAC | refinement |
ARP/wARP | model building |
MOSFLM | data reduction |
SCALA | data scaling |
CHAINSAW | phasing |
REFMAC | phasing |