6R3O

Aspergillus niger ferric acid decarboxylase (Fdc) L439G variant in complex with prFMN (purified in the radical form) and phenylpropiolic 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 PROPANE 6.5, 20 % W/V PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3948.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.83α = 90
b = 64.1β = 90
c = 87.61γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2017-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.98DiamondI04

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
11.1347.9299.90.99911.485.3201245
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)
11.131.1799.810.5731.414.8

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 SYNTHESISTHROUGHOUT4ZA91.1347.921911821006299.90.151020.150020.17049RANDOM14.536
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]
-0.520.74-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.978
r_dihedral_angle_4_deg20.474
r_dihedral_angle_3_deg12.172
r_long_range_B_refined9.046
r_long_range_B_other9.04
r_dihedral_angle_1_deg6.571
r_scangle_other3.483
r_scbond_it2.518
r_scbond_other2.517
r_angle_refined_deg2.495
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.978
r_dihedral_angle_4_deg20.474
r_dihedral_angle_3_deg12.172
r_long_range_B_refined9.046
r_long_range_B_other9.04
r_dihedral_angle_1_deg6.571
r_scangle_other3.483
r_scbond_it2.518
r_scbond_other2.517
r_angle_refined_deg2.495
r_mcangle_it1.782
r_mcangle_other1.782
r_angle_other_deg1.267
r_mcbond_it1.262
r_mcbond_other1.262
r_chiral_restr0.18
r_bond_refined_d0.028
r_gen_planes_refined0.019
r_gen_planes_other0.01
r_bond_other_d0.003
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 Atoms3848
Nucleic Acid Atoms
Solvent Atoms727
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling