6R2R

Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with prFMN (purified in dark) and alphafluorocinnamic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM THIOCYANATE, BIS-TRIS PROPANE 6.5, 20 % W/V PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3848.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.681α = 90
b = 63.945β = 90
c = 87.573γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2018-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.916DiamondI04-1

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
11.10351.6488.40.0650.99810.75190502
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)
11.1031.14261.060.580.70224.3

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 SYNTHESISTHROUGHOUT4ZA91.1351.64180930957488.390.120270.119110.14184RANDOM12.889
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]
0.63-1.190.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.055
r_sphericity_free23.565
r_dihedral_angle_4_deg20.836
r_sphericity_bonded12.412
r_dihedral_angle_3_deg12.009
r_rigid_bond_restr11.242
r_dihedral_angle_1_deg6.613
r_long_range_B_refined4.135
r_scbond_it4.102
r_scbond_other4.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.055
r_sphericity_free23.565
r_dihedral_angle_4_deg20.836
r_sphericity_bonded12.412
r_dihedral_angle_3_deg12.009
r_rigid_bond_restr11.242
r_dihedral_angle_1_deg6.613
r_long_range_B_refined4.135
r_scbond_it4.102
r_scbond_other4.102
r_long_range_B_other4.079
r_scangle_other3.805
r_mcbond_other2.538
r_mcbond_it2.536
r_mcangle_other2.424
r_mcangle_it2.418
r_angle_refined_deg1.891
r_angle_other_deg1.174
r_chiral_restr0.312
r_bond_refined_d0.016
r_gen_planes_refined0.012
r_bond_other_d0.004
r_gen_planes_other0.004
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 Atoms3847
Nucleic Acid Atoms
Solvent Atoms622
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling