6R3L

Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and cinnamic acid following decarboxylation (Int3)


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
2.448.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.923α = 90
b = 64.219β = 90
c = 87.773γ = 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)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
11.2487.7799.87.414.3153420
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.241.281.76

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 SYNTHESISTHROUGHOUT4ZA91.2487.77145843755199.80.1320.130.167RANDOM12.99
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]
0.01-0.150.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.446
r_sphericity_free24.207
r_dihedral_angle_4_deg21.517
r_dihedral_angle_3_deg11.738
r_sphericity_bonded7.299
r_dihedral_angle_1_deg6.585
r_rigid_bond_restr5.265
r_long_range_B_refined3.906
r_long_range_B_other3.906
r_scangle_other2.771
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.446
r_sphericity_free24.207
r_dihedral_angle_4_deg21.517
r_dihedral_angle_3_deg11.738
r_sphericity_bonded7.299
r_dihedral_angle_1_deg6.585
r_rigid_bond_restr5.265
r_long_range_B_refined3.906
r_long_range_B_other3.906
r_scangle_other2.771
r_scbond_it2.56
r_scbond_other2.56
r_angle_refined_deg2.357
r_mcangle_other1.737
r_mcangle_it1.733
r_mcbond_it1.474
r_mcbond_other1.474
r_angle_other_deg1.29
r_chiral_restr0.452
r_bond_refined_d0.026
r_gen_planes_refined0.016
r_gen_planes_other0.006
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 Atoms3852
Nucleic Acid Atoms
Solvent Atoms699
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling