6TIH

Structure of A. niger Fdc WT in complex with 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
2.4148.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.72α = 90
b = 63.611β = 90
c = 87.627γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.916DiamondI04-1

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
11.0245.37896.50.077110.15.2218173
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)
11.021.0971.70.7850.71.6

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-VALUE4ZAA1.02145.3782181731090080.7250.1230.12250.141713.054
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]
0.074-0.2460.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.774
r_dihedral_angle_4_deg20.451
r_dihedral_angle_3_deg11.482
r_rigid_bond_restr10.229
r_dihedral_angle_1_deg6.851
r_scbond_it4.839
r_scbond_other4.838
r_scangle_it4.767
r_scangle_other4.766
r_lrange_it4.746
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.774
r_dihedral_angle_4_deg20.451
r_dihedral_angle_3_deg11.482
r_rigid_bond_restr10.229
r_dihedral_angle_1_deg6.851
r_scbond_it4.839
r_scbond_other4.838
r_scangle_it4.767
r_scangle_other4.766
r_lrange_it4.746
r_lrange_other4.746
r_mcangle_other3.392
r_mcangle_it3.391
r_mcbond_it2.678
r_mcbond_other2.668
r_angle_refined_deg2.276
r_angle_other_deg1.689
r_nbd_refined0.313
r_symmetry_xyhbond_nbd_refined0.302
r_xyhbond_nbd_refined0.262
r_nbd_other0.244
r_symmetry_nbd_refined0.228
r_symmetry_nbd_other0.199
r_nbtor_refined0.183
r_chiral_restr0.151
r_symmetry_xyhbond_nbd_other0.124
r_symmetry_nbtor_other0.092
r_metal_ion_refined0.088
r_gen_planes_refined0.024
r_bond_refined_d0.023
r_gen_planes_other0.006
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3852
Nucleic Acid Atoms
Solvent Atoms630
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling