8OED

Aspergillus niger ferulic acid decarboxylase (Fdc) S145C-P289C (DB2) variant in complex with prenylated flavin hydroxylated at the C1 prime position


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4ZA4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277BIS-TRIS propane, potassium thiocyanate, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3948.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.879α = 90
b = 63.995β = 90
c = 87.708γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.3787.7198110.912.91458231
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)
11.371.390.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.3787.7188815467581.980.151520.150740.166RANDOM13.772
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]
-0.080.070.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.391
r_dihedral_angle_2_deg11.115
r_dihedral_angle_1_deg6.485
r_long_range_B_refined5.132
r_long_range_B_other5.132
r_scangle_other3.06
r_scbond_other2.13
r_scbond_it2.129
r_mcangle_it1.826
r_mcangle_other1.826
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.391
r_dihedral_angle_2_deg11.115
r_dihedral_angle_1_deg6.485
r_long_range_B_refined5.132
r_long_range_B_other5.132
r_scangle_other3.06
r_scbond_other2.13
r_scbond_it2.129
r_mcangle_it1.826
r_mcangle_other1.826
r_angle_refined_deg1.748
r_mcbond_it1.266
r_mcbond_other1.265
r_angle_other_deg0.604
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_4_deg
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3846
Nucleic Acid Atoms
Solvent Atoms547
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing