6R34
Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and phenyl acetylene (Int3')
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4ZA9 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | 0.2 M POTASSIUM THIOCYANATE, BIS-TRIS PROPANE 6.5, 20 % W/V PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 96 | α = 90 |
b = 63.96 | β = 90 |
c = 87.72 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 300K | 2017-01-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.98 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.1 | 45.51 | 96.7 | 0.997 | 9.72 | 4 | 211213 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.1 | 1.139 | 77.13 | 0.552 | 1.44 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 4ZA9 | 1.1 | 45.51 | 200575 | 10639 | 96.71 | 0.11731 | 0.11608 | 0.14059 | RANDOM | 12.647 |
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] | |
-0.33 | 0.41 | -0.08 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.707 |
r_sphericity_free | 26.435 |
r_dihedral_angle_4_deg | 20.976 |
r_dihedral_angle_3_deg | 11.625 |
r_sphericity_bonded | 8.433 |
r_dihedral_angle_1_deg | 6.561 |
r_rigid_bond_restr | 4.78 |
r_long_range_B_refined | 3.464 |
r_long_range_B_other | 3.372 |
r_scangle_other | 2.773 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3852 |
Nucleic Acid Atoms | |
Solvent Atoms | 733 |
Heterogen Atoms | 47 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
xia2 | data scaling |