6TIE

Structure of A. niger Fdc I327S variant 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
2.4249.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.703α = 90
b = 63.798β = 90
c = 87.7γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-07-14MSINGLE 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
11.0687.795.90.172166.6196014
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)
11.061.1275.91.0160.71.5

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-VALUE4ZAA1.0687.7196014977378.8330.1360.13460.158112.073
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]
0.171-0.7430.571
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.158
r_dihedral_angle_4_deg21.898
r_dihedral_angle_3_deg11.768
r_rigid_bond_restr9.12
r_dihedral_angle_1_deg6.809
r_lrange_it4.171
r_lrange_other4.171
r_scangle_it3.905
r_scangle_other3.904
r_scbond_it3.688
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.158
r_dihedral_angle_4_deg21.898
r_dihedral_angle_3_deg11.768
r_rigid_bond_restr9.12
r_dihedral_angle_1_deg6.809
r_lrange_it4.171
r_lrange_other4.171
r_scangle_it3.905
r_scangle_other3.904
r_scbond_it3.688
r_scbond_other3.688
r_mcangle_other2.279
r_mcangle_it2.277
r_angle_refined_deg2.227
r_mcbond_it2.093
r_mcbond_other2.093
r_angle_other_deg1.693
r_nbd_refined0.272
r_symmetry_xyhbond_nbd_refined0.246
r_nbd_other0.231
r_symmetry_nbd_other0.198
r_symmetry_nbd_refined0.192
r_xyhbond_nbd_refined0.186
r_nbtor_refined0.181
r_xyhbond_nbd_other0.156
r_symmetry_xyhbond_nbd_other0.149
r_chiral_restr0.142
r_symmetry_nbtor_other0.091
r_metal_ion_refined0.084
r_gen_planes_refined0.025
r_bond_refined_d0.021
r_gen_planes_other0.006
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3850
Nucleic Acid Atoms
Solvent Atoms611
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling