6EV4

Structure of wild type A. niger Fdc1 purified in the dark with prFMN in the iminium form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3948.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.97α = 90
b = 64.03β = 90
c = 87.63γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1.9795DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.1447.9994.99.83.6186270
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.141.1810.8072.4

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 DIFFRACTIONTHROUGHOUT1.1447.98176880934994.850.149650.148720.16732RANDOM11.826
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]
-0.180.31-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.706
r_dihedral_angle_4_deg19.605
r_long_range_B_refined15.53
r_long_range_B_other13.031
r_dihedral_angle_3_deg12.256
r_dihedral_angle_1_deg6.595
r_scangle_other2.872
r_angle_refined_deg2.417
r_scbond_it2.078
r_scbond_other2.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.706
r_dihedral_angle_4_deg19.605
r_long_range_B_refined15.53
r_long_range_B_other13.031
r_dihedral_angle_3_deg12.256
r_dihedral_angle_1_deg6.595
r_scangle_other2.872
r_angle_refined_deg2.417
r_scbond_it2.078
r_scbond_other2.077
r_mcangle_it1.536
r_mcangle_other1.536
r_angle_other_deg1.244
r_mcbond_it1.084
r_mcbond_other1.084
r_chiral_restr0.177
r_bond_refined_d0.026
r_gen_planes_refined0.019
r_gen_planes_other0.009
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 Atoms3852
Nucleic Acid Atoms
Solvent Atoms845
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing