4ESJ
RESTRICTION ENDONUCLEASE DpnI 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 | 6.8 | 293 | 200 MM POTASSIUM SULFATE, 100 MM BETAINE, 20 % W/V PEG 3350, PH 6.8. FOR CRYOCOOLING THE CRYSTALLIZATION BUFFER WAS MIXED IN 3:1 RATIO WITH 100% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.44 | 64.29 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 130.518 | α = 90 |
b = 98.411 | β = 112.21 |
c = 83.884 | 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 Q315 | BENT MIRRORS | 2010-12-05 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I02 | 0.97949,1.2833,1.2835 | 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 | 2.05 | 20 | 98 | 0.028 | 0.028 | 17.5 | 2.9 | 60190 | 60190 |
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 | 2.05 | 2.1 | 98.4 | 0.3 | 0.3 | 2.4 | 3 | 4429 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 2.05 | 19.97 | 60188 | 60188 | 3032 | 100 | 0.19872 | 0.19872 | 0.19772 | 0.21754 | RANDOM | 51.616 |
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] | |
0.45 | -0.81 | -0.44 | -0.62 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.568 |
r_dihedral_angle_4_deg | 19.503 |
r_dihedral_angle_3_deg | 14.768 |
r_dihedral_angle_1_deg | 6.112 |
r_angle_other_deg | 3.954 |
r_scangle_it | 2.725 |
r_scbond_it | 1.736 |
r_angle_refined_deg | 1.24 |
r_mcangle_it | 1.201 |
r_mcbond_it | 0.657 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4036 |
Nucleic Acid Atoms | 730 |
Solvent Atoms | 197 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SHELXDE | phasing |
DM | model building |
ARP/wARP | model building |
REFMAC | refinement |
CNS | refinement |
XDS | data reduction |
SCALA | data scaling |
DM | phasing |