6TIN
Structure of A. niger Fdc WT in complex with FMN and indole 2 carboxylic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4ZAA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.43 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 95.894 | ¦Á = 90 |
b = 63.934 | ¦Â = 90 |
c = 87.668 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 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 | PIXEL | DECTRIS PILATUS 6M-F | 2018-02-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.975 | 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 | 1.28 | 64.79 | 100 | 0.12 | 1 | 8.5 | 6.4 | 139040 |
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 | 1.28 | 1.3 | 98.9 | 0.818 | 0.5 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | FREE R-VALUE | 4ZAA | 1.28 | 64.704 | 137282 | 6826 | 98.717 | 0.162 | 0.1604 | 0.1976 | 11.866 |
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] | |
0.117 | -0.174 | 0.057 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.6 |
r_dihedral_angle_4_deg | 21.753 |
r_dihedral_angle_3_deg | 12.341 |
r_dihedral_angle_1_deg | 6.776 |
r_rigid_bond_restr | 4.981 |
r_lrange_it | 3.999 |
r_lrange_other | 3.999 |
r_scangle_it | 3.33 |
r_scangle_other | 3.329 |
r_scbond_it | 2.931 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3807 |
Nucleic Acid Atoms | |
Solvent Atoms | 464 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
DIALS | data scaling |