6X1J
The homing endonuclease I-WcaI bound to its DNA recognition sequence
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | 21% PEG 3350, 0.1M Tris-HCl, 0.2M Lithium sulfate, 2 mM DTT |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.09 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 67.601 | α = 90 |
b = 37.281 | β = 100.44 |
c = 94.064 | γ = 90 |
Symmetry | |
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Space Group | P 1 2 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 | RAYONIX MX300HE | 2016-02-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | 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 | 1.945 | 30 | 99.8 | 0.198 | 0.104 | 0.964 | 6.5 | 3.6 | 33735 | 33.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.945 | 2.02 | 99.6 | 0.72 | 0.858 | 0.461 | 0.807 | 1.6 | 3.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 1R7M | 1.945 | 29.88 | 31986 | 1627 | 97.49 | 0.229 | 0.2272 | 0.2612 | RANDOM | 37.752 |
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] | |
0.05 | -0.01 | -0.02 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.759 |
r_dihedral_angle_3_deg | 17.935 |
r_dihedral_angle_1_deg | 8.073 |
r_dihedral_angle_4_deg | 8.072 |
r_angle_refined_deg | 1.76 |
r_angle_other_deg | 1.407 |
r_chiral_restr | 0.136 |
r_gen_planes_refined | 0.011 |
r_bond_refined_d | 0.009 |
r_gen_planes_other | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1926 |
Nucleic Acid Atoms | 1004 |
Solvent Atoms | 141 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
PDB_EXTRACT | data extraction |