6Q32
The structure of the Mo-insertase domain Cnx1E (variant S269DD274S) from Arabidopsis thaliana in complex with Moco-AMP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5G2S |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 294 | 0.1 M MES pH 6.5, 24 % (v/v) PEG 400; in an anoxic atmosphere containing a 95 % argon and 5 % hydrogen gas |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.27 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.01 | α = 90 |
b = 123.29 | β = 90 |
c = 133.14 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 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 | PIXEL | DECTRIS PILATUS 6M | Rh coated collimating mirrors, K-B focusing mirrors | 2014-10-02 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Rh coated collimating mirrors, K-B focusing mirrors | 2014-10-02 | M | SINGLE WAVELENGTH | |||||
3 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | Rh coated collimating mirrors, K-B focusing mirrors | 2014-10-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.99987 | SSRL | BL12-2 |
2 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.99987 | SSRL | BL12-2 |
3 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 1.74262 | SSRL | BL12-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | ||||||
2 | 1.386 | 20.32 | 99 | 0.1846 | 0.1919 | 0.991 | 16.05 | 13.1 | 106766 | -3 | 21.97 |
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) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
2 | 1.386 | 1.44 | 96 | 6.111 | 6.44 | 0.116 | 0.18 | 10.1 |
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 | 5G2S | 1.39 | 20.35 | 80115 | 3902 | 74.6 | 0.16 | 0.159 | 0.177 | RANDOM | 27.59 |
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] | |
-1.0434 | 0.9461 | 0.0973 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 12.69 |
t_omega_torsion | 4.46 |
t_angle_deg | 1.13 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3107 |
Nucleic Acid Atoms | |
Solvent Atoms | 435 |
Heterogen Atoms | 73 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
STARANISO | data scaling |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |