6TIN

Structure of A. niger Fdc WT in complex with FMN and indole 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
2.3948.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.894α = 90
b = 63.934β = 90
c = 87.668γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.975DiamondI04

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
11.2864.791000.1218.56.4139040
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)
11.281.398.90.8180.51.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE4ZAA1.2864.704137282682698.7170.1620.16040.197611.866
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]
0.117-0.1740.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.6
r_dihedral_angle_4_deg21.753
r_dihedral_angle_3_deg12.341
r_dihedral_angle_1_deg6.776
r_rigid_bond_restr4.981
r_lrange_it3.999
r_lrange_other3.999
r_scangle_it3.33
r_scangle_other3.329
r_scbond_it2.931
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.6
r_dihedral_angle_4_deg21.753
r_dihedral_angle_3_deg12.341
r_dihedral_angle_1_deg6.776
r_rigid_bond_restr4.981
r_lrange_it3.999
r_lrange_other3.999
r_scangle_it3.33
r_scangle_other3.329
r_scbond_it2.931
r_scbond_other2.931
r_mcangle_it2.415
r_mcangle_other2.414
r_angle_refined_deg2.223
r_mcbond_it2.065
r_mcbond_other2.065
r_angle_other_deg1.681
r_nbd_refined0.247
r_symmetry_xyhbond_nbd_refined0.24
r_nbd_other0.225
r_symmetry_nbd_refined0.215
r_symmetry_nbd_other0.193
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.166
r_chiral_restr0.129
r_metal_ion_refined0.119
r_symmetry_nbtor_other0.088
r_symmetry_xyhbond_nbd_other0.039
r_symmetry_metal_ion_refined0.022
r_bond_refined_d0.019
r_gen_planes_refined0.017
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3807
Nucleic Acid Atoms
Solvent Atoms464
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling