6TIO

Structure of A. niger Fdc Wt in complex with FMN and benzothiophene 2 carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3447.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.39α = 90
b = 63.283β = 90
c = 87.501γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
11.5495.5799.80.13616.9578889
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.570.8160.51.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE4ZAA1.5464.48278838386999.7360.150.14790.195118.2
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]
0.328-0.4490.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.54
r_dihedral_angle_4_deg22.344
r_dihedral_angle_3_deg12.437
r_dihedral_angle_1_deg6.788
r_lrange_it4.663
r_lrange_other4.662
r_rigid_bond_restr3.838
r_scangle_it3.745
r_scangle_other3.742
r_mcangle_other3.405
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.54
r_dihedral_angle_4_deg22.344
r_dihedral_angle_3_deg12.437
r_dihedral_angle_1_deg6.788
r_lrange_it4.663
r_lrange_other4.662
r_rigid_bond_restr3.838
r_scangle_it3.745
r_scangle_other3.742
r_mcangle_other3.405
r_mcangle_it3.404
r_scbond_it3.291
r_scbond_other3.291
r_mcbond_it2.841
r_mcbond_other2.835
r_angle_refined_deg1.98
r_angle_other_deg1.59
r_symmetry_nbd_refined0.245
r_nbd_refined0.239
r_symmetry_xyhbond_nbd_refined0.238
r_nbd_other0.222
r_xyhbond_nbd_refined0.197
r_symmetry_nbd_other0.194
r_nbtor_refined0.171
r_chiral_restr0.113
r_metal_ion_refined0.102
r_symmetry_nbtor_other0.085
r_symmetry_metal_ion_refined0.076
r_symmetry_xyhbond_nbd_other0.038
r_bond_refined_d0.016
r_gen_planes_refined0.014
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3807
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling