5I3E
Crystal structure of putative Putative deoxyribonuclease-2 from Burkholderia thailandensis, E264
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 290 | MCSG1 screen, b12: 100mM BisTris pH 6.5, 28% PEG MME 2000, trays set up at 26.5mg/ml, cryo: 15% EG; for phasing a crystal from 25% PEG 3350, 100mM BisTris pH 6.0 was incubated for 30s in a buffer containing 15% EG and 750mM NaI, iodide data were collected at the in-house source; ButhA.18065.a.B1.PS18111 at 26.5 mg/ml |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.04 | 39.58 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.16 | α = 90 |
b = 61.75 | β = 92.12 |
c = 102.6 | 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 315 | 2013-09-25 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | RIGAKU SATURN 944+ | 2013-10-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 8.2.2 | 0.999995 | ALS | 8.2.2 |
2 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | 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 | 1.65 | 50 | 98.7 | 0.052 | 0.998 | 16.74 | 2.5 | 76021 | -3 | 12.12 |
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 | 1.65 | 1.69 | 99.5 | 0.523 | 2.12 | 2.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | SAD | FREE R-VALUE | 1.65 | 39.443 | 1.35 | 76000 | 3745 | 98.7 | 0.1557 | 0.1541 | 0.1866 | 19.2921 |
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 |
f_dihedral_angle_d | 11.377 |
f_angle_d | 0.886 |
f_chiral_restr | 0.058 |
f_bond_d | 0.006 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5379 |
Nucleic Acid Atoms | |
Solvent Atoms | 739 |
Heterogen Atoms | 8 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XSCALE | data scaling |
PHASER | phasing |
ARP | model building |
REFMAC | refinement |
XDS | data scaling |
Coot | model building |