6TIC

Structure of A. niger Fdc I327S variant 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
2.3948.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.571α = 90
b = 63.357β = 90
c = 87.594γ = 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
11.2887.59494.60.10419.46.4107134
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)
11.281.3757.11.1160.61.56.4

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-VALUE4ZAA1.28187.59107134523778.1730.1620.15920.210817.43
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]
-0.239-0.6160.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.821
r_dihedral_angle_4_deg23.249
r_dihedral_angle_3_deg12.947
r_dihedral_angle_1_deg7.179
r_scangle_it5.311
r_scangle_other5.31
r_rigid_bond_restr5.219
r_scbond_it4.969
r_scbond_other4.968
r_lrange_it4.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.821
r_dihedral_angle_4_deg23.249
r_dihedral_angle_3_deg12.947
r_dihedral_angle_1_deg7.179
r_scangle_it5.311
r_scangle_other5.31
r_rigid_bond_restr5.219
r_scbond_it4.969
r_scbond_other4.968
r_lrange_it4.95
r_lrange_other4.751
r_mcangle_other3.702
r_mcangle_it3.694
r_mcbond_it3.127
r_mcbond_other3.08
r_angle_refined_deg2.061
r_angle_other_deg1.605
r_nbd_refined0.262
r_nbd_other0.219
r_symmetry_nbd_other0.206
r_symmetry_nbd_refined0.201
r_xyhbond_nbd_refined0.192
r_nbtor_refined0.175
r_symmetry_xyhbond_nbd_refined0.16
r_chiral_restr0.115
r_metal_ion_refined0.1
r_symmetry_nbtor_other0.087
r_gen_planes_refined0.018
r_bond_refined_d0.015
r_gen_planes_other0.006
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3850
Nucleic Acid Atoms
Solvent Atoms551
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling