3AJV
Splicing endonuclease from Aeropyrum pernix
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 295 | 20mM Tris-HCl (pH 8.0), 750mM KCl, 10% (v/v) glycerol, 0.2M NaCl, 0.1M phosphate-citrate (pH 4.2), 10% (w/v) PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.19 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.334 | α = 90 |
b = 95.334 | β = 90 |
c = 253.819 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 270 | 2008-12-13 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 270 | 2008-11-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 1 | Photon Factory | BL-17A |
2 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 1.0717 | Photon Factory | BL-17A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.7 | 50 | 98.5 | 0.072 | 14 | 4.8 | 92608 | 90770 |
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) | |||||||||||
1,2 | 1.7 | 1.73 | 85.1 | 0.346 | 3.1 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | SIRAS | THROUGHOUT | 1.7 | 30 | 92608 | 88149 | 4695 | 98.29 | 0.21809 | 0.21809 | 0.21751 | 0.22893 | RANDOM | 23.45 |
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] | |
4.14 | 4.14 | -8.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.09 |
r_dihedral_angle_4_deg | 20.071 |
r_dihedral_angle_3_deg | 15.07 |
r_dihedral_angle_1_deg | 6.227 |
r_scangle_it | 3.965 |
r_scbond_it | 2.475 |
r_mcangle_it | 1.589 |
r_angle_refined_deg | 1.505 |
r_mcbond_it | 0.944 |
r_chiral_restr | 0.105 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5336 |
Nucleic Acid Atoms | |
Solvent Atoms | 549 |
Heterogen Atoms | 62 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SHELXCD | phasing |
SHELXE | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |