5ODJ
Single-stranded DNA-binding protein from bacteriophage Enc34
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293 | 0.1 M Bis-tris methane, 0.3 M MgCl2, 20% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 43.11 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 38.08 | α = 90 |
b = 67.2 | β = 90 |
c = 76.83 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 2013-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | MAX II BEAMLINE I911-3 | 0.97671 | MAX II | I911-3 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | 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 | 1.5 | 30.78 | 99.4 | 0.104 | 0.062 | 0.989 | 6.9 | 3.6 | 32072 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.5 | 1.58 | 100 | 0.77 | 0.464 | 0.579 | 2.5 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.5 | 30.78 | 30418 | 1579 | 98.99 | 0.15819 | 0.1565 | 0.19255 | RANDOM | 23.687 |
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] | |
0.55 | 1.95 | -2.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 31.15 |
r_dihedral_angle_2_deg | 28.542 |
r_dihedral_angle_4_deg | 20.027 |
r_dihedral_angle_3_deg | 12.018 |
r_rigid_bond_restr | 11.983 |
r_sphericity_bonded | 10.162 |
r_dihedral_angle_1_deg | 6.272 |
r_long_range_B_refined | 3.998 |
r_long_range_B_other | 3.768 |
r_angle_other_deg | 3.606 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1424 |
Nucleic Acid Atoms | |
Solvent Atoms | 170 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
SHELXD | phasing |