6TSC
OphMA I407P complex with SAH
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 289 | 0.3-0.4 M KSCN, 0.1 M Bicine pH 8-9, 1.8-2.5 M sodium malonate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.86 | 68.15 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.379 | α = 90 |
b = 89.379 | β = 90 |
c = 157.001 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | PIXEL | DECTRIS EIGER X 16M | 2019-05-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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) | Rrim 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 | 2.19 | 52.33 | 100 | 0.058 | 1 | 15.7 | 11.1 | 38116 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.19 | 2.23 | 99.7 | 2.088 | 0.9 | 1.1 | 10.9 |
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 | 5N0O | 2.19 | 52.33 | 36209 | 1846 | 99.93 | 0.209 | 0.2078 | 0.2322 | RANDOM | 99.841 |
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] | |
2.87 | 1.44 | 2.87 | -9.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.789 |
r_dihedral_angle_4_deg | 20.355 |
r_dihedral_angle_3_deg | 15.709 |
r_dihedral_angle_1_deg | 6.939 |
r_angle_refined_deg | 1.518 |
r_angle_other_deg | 1.192 |
r_chiral_restr | 0.063 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.006 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2960 |
Nucleic Acid Atoms | |
Solvent Atoms | 3 |
Heterogen Atoms | 26 |
Software
Software | |
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Software Name | Purpose |
xia2 | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
PHASER | phasing |