5OMT
Endonuclease NucB
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 100 mM MES pH6.5 12% PEG 20000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.49 | 50.62 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.955 | α = 90 |
b = 59.955 | β = 90 |
c = 66.604 | 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 | 2012-07-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.35 | 44.56 | 100 | 0.991 | 16.1 | 7.8 | 27361 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.35 | 1.37 | 100 | 0.944 | 3.6 | 7.7 |
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 | SAD | THROUGHOUT | 1.35 | 44.56 | 25934 | 1369 | 100 | 0.15034 | 0.1485 | 0.18623 | RANDOM | 18.443 |
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] | |
-0.79 | -0.79 | 1.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.634 |
r_sphericity_free | 18.023 |
r_dihedral_angle_3_deg | 12.034 |
r_dihedral_angle_4_deg | 10.784 |
r_sphericity_bonded | 10.774 |
r_dihedral_angle_1_deg | 5.752 |
r_long_range_B_refined | 4.521 |
r_long_range_B_other | 4.424 |
r_scangle_other | 3.901 |
r_scbond_it | 3.458 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 839 |
Nucleic Acid Atoms | |
Solvent Atoms | 104 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
Aimless | data scaling |
SHELXCD | phasing |
SHELXE | model building |
ARP/wARP | model building |
BUCCANEER | model building |
REFMAC | refinement |
Coot | model building |