6R30

Aspergillus niger ferulic acid decarboxylase (Fdc) L439G variant in complex with the covalent adduct formed between prFMN cofactor and phenylpropiolic acid (Int1')


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZA9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M POTASSIUM THIOCYANATE, BIS-TRIS PROPANE 6.5, 20 % W/V PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4148.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.01α = 90
b = 64.37β = 90
c = 87.81γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2018-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.1239.9399.250.9977.954.3207057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.121.160.591.32

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4ZA91.1239.931967091034899.260.125560.124220.15046RANDOM13.429
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]
-0.23-0.170.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.194
r_sphericity_free25.916
r_dihedral_angle_4_deg20.427
r_dihedral_angle_3_deg11.963
r_sphericity_bonded9.766
r_dihedral_angle_1_deg6.56
r_rigid_bond_restr4.978
r_long_range_B_refined3.771
r_scangle_other3.417
r_scbond_it3.363
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.194
r_sphericity_free25.916
r_dihedral_angle_4_deg20.427
r_dihedral_angle_3_deg11.963
r_sphericity_bonded9.766
r_dihedral_angle_1_deg6.56
r_rigid_bond_restr4.978
r_long_range_B_refined3.771
r_scangle_other3.417
r_scbond_it3.363
r_scbond_other3.361
r_long_range_B_other3.063
r_angle_refined_deg2.031
r_mcangle_other1.885
r_mcangle_it1.884
r_mcbond_it1.505
r_mcbond_other1.505
r_angle_other_deg1.248
r_chiral_restr0.396
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3850
Nucleic Acid Atoms
Solvent Atoms731
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling