6R2P

Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with FMN and cinnamic acid


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 REMARK 280 PROPANE 6.5, 20 % W/V PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3848.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.895α = 90
b = 63.835β = 90
c = 87.651γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.98DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.2653.1498.90.0840.9988.654.3144955
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.261.30597.550.63770.8721.664.1

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 SYNTHESISTHROUGHOUT4ZA91.2653.14136775718198.810.152680.150870.18701RANDOM11.036
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]
-0.360.42-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.425
r_dihedral_angle_4_deg22.569
r_sphericity_free16.691
r_dihedral_angle_3_deg12.061
r_dihedral_angle_1_deg6.697
r_rigid_bond_restr6.633
r_sphericity_bonded6.042
r_long_range_B_refined2.954
r_long_range_B_other2.954
r_scangle_other2.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.425
r_dihedral_angle_4_deg22.569
r_sphericity_free16.691
r_dihedral_angle_3_deg12.061
r_dihedral_angle_1_deg6.697
r_rigid_bond_restr6.633
r_sphericity_bonded6.042
r_long_range_B_refined2.954
r_long_range_B_other2.954
r_scangle_other2.61
r_angle_refined_deg2.546
r_scbond_it2.398
r_scbond_other2.397
r_mcangle_it2.094
r_mcangle_other2.094
r_mcbond_it1.839
r_mcbond_other1.835
r_angle_other_deg1.251
r_chiral_restr0.169
r_bond_refined_d0.028
r_gen_planes_refined0.018
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 Atoms3807
Nucleic Acid Atoms
Solvent Atoms466
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling