5ZMM
Structure of the Type IV phosphorothioation-dependent restriction endonuclease ScoMcrA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 287 | 0.2M lithium sulfate, 0.1M Tris-HCl, pH 8.5, 13% (w/v) polyethylene glycol (PEG) 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.42 | 64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 130.183 | α = 90 |
b = 139.367 | β = 90 |
c = 281.005 | 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 | ADSC QUANTUM 315r | 2011-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U1 | 0.97892 | SSRF | BL17U1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.15 | 140.5 | 99.9 | 12.8 | 5.7 | 88897 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 3.15 | 3.26 |
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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 3.15 | 140.5 | 74915 | 3796 | 88.24 | 0.2467 | 0.245 | 0.24 | 0.2799 | 0.28 | RANDOM | 69.705 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[2][2] | Anisotropic B[3][3] | ||||
0.63 | 0.6 | -1.23 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.493 |
r_dihedral_angle_3_deg | 18.934 |
r_dihedral_angle_4_deg | 15.203 |
r_dihedral_angle_1_deg | 11.148 |
r_angle_refined_deg | 1.568 |
r_angle_other_deg | 1.034 |
r_chiral_restr | 0.085 |
r_bond_refined_d | 0.013 |
r_bond_other_d | 0.007 |
r_gen_planes_refined | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 23267 |
Nucleic Acid Atoms | |
Solvent Atoms | 24 |
Heterogen Atoms | 61 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |