6TIJ

Structure of A. niger Fdc WT in complex with indol-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
2.4249.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.781α = 90
b = 63.725β = 90
c = 87.707γ = 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
11.1264.7999.50.09319.36204931
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)
11.121.1491.90.7390.51.5

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-VALUE4ZAA1.1264.6852028051001298.5130.1410.13970.168612.659
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]
-0.022-0.1490.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.405
r_dihedral_angle_4_deg21.99
r_dihedral_angle_3_deg11.803
r_dihedral_angle_1_deg6.783
r_rigid_bond_restr5.227
r_lrange_it4.183
r_lrange_other4.183
r_scangle_other3.633
r_scangle_it3.632
r_scbond_it3.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.405
r_dihedral_angle_4_deg21.99
r_dihedral_angle_3_deg11.803
r_dihedral_angle_1_deg6.783
r_rigid_bond_restr5.227
r_lrange_it4.183
r_lrange_other4.183
r_scangle_other3.633
r_scangle_it3.632
r_scbond_it3.117
r_scbond_other3.117
r_angle_refined_deg2.224
r_mcangle_other2.194
r_mcangle_it2.191
r_mcbond_it2.014
r_mcbond_other2.004
r_angle_other_deg1.686
r_symmetry_xyhbond_nbd_refined0.302
r_nbd_refined0.254
r_xyhbond_nbd_other0.231
r_nbd_other0.225
r_xyhbond_nbd_refined0.22
r_symmetry_nbd_refined0.212
r_symmetry_nbd_other0.2
r_nbtor_refined0.181
r_chiral_restr0.149
r_metal_ion_refined0.092
r_symmetry_nbtor_other0.09
r_gen_planes_refined0.024
r_bond_refined_d0.02
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3852
Nucleic Acid Atoms
Solvent Atoms656
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling