6R2Z

Aspergillus niger ferulic acid decarboxylase (Fdc) F437L 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
2.3948.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.734α = 90
b = 64.133β = 90
c = 87.574γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2018-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.916DiamondI04-1

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
11.0864.6277.990.97795.5179369
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)
11.081.1970.635.5

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 SYNTHESISTHROUGHOUT4ZA91.0864.62170470890377.580.131670.130540.15339RANDOM11.753
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]
-0.14-1.561.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.739
r_sphericity_free28.277
r_dihedral_angle_4_deg22.277
r_sphericity_bonded12.935
r_dihedral_angle_3_deg11.587
r_rigid_bond_restr9.144
r_dihedral_angle_1_deg6.592
r_long_range_B_refined3.956
r_long_range_B_other3.809
r_scangle_other2.735
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.739
r_sphericity_free28.277
r_dihedral_angle_4_deg22.277
r_sphericity_bonded12.935
r_dihedral_angle_3_deg11.587
r_rigid_bond_restr9.144
r_dihedral_angle_1_deg6.592
r_long_range_B_refined3.956
r_long_range_B_other3.809
r_scangle_other2.735
r_scbond_it2.357
r_scbond_other2.357
r_angle_refined_deg1.909
r_mcangle_other1.782
r_mcangle_it1.781
r_mcbond_other1.486
r_mcbond_it1.484
r_angle_other_deg1.21
r_chiral_restr0.394
r_bond_refined_d0.024
r_gen_planes_refined0.014
r_gen_planes_other0.004
r_bond_other_d0.001
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 Atoms3851
Nucleic Acid Atoms
Solvent Atoms733
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling