6TIL

Structure of A. niger Fdc WT in complex with FMN and 2 naphthoic 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
2.3447.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.628α = 90
b = 63.183β = 90
c = 87.318γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.90DiamondI03

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
11.4264.5599.30.12316.44.499700
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)
11.421.4497.60.7920.61.64.4

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-VALUE4ZAA1.4264.48199668491999.3010.1540.15170.199716.807
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]
0.286-0.460.174
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.728
r_dihedral_angle_4_deg21.4
r_dihedral_angle_3_deg12.256
r_dihedral_angle_1_deg6.824
r_rigid_bond_restr4.487
r_lrange_it4.452
r_lrange_other4.451
r_scangle_other3.637
r_scangle_it3.634
r_scbond_it3.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.728
r_dihedral_angle_4_deg21.4
r_dihedral_angle_3_deg12.256
r_dihedral_angle_1_deg6.824
r_rigid_bond_restr4.487
r_lrange_it4.452
r_lrange_other4.451
r_scangle_other3.637
r_scangle_it3.634
r_scbond_it3.206
r_scbond_other3.206
r_mcangle_other2.849
r_mcangle_it2.846
r_mcbond_it2.471
r_mcbond_other2.46
r_angle_refined_deg2.006
r_angle_other_deg1.614
r_symmetry_nbd_refined0.26
r_nbd_refined0.244
r_nbd_other0.24
r_symmetry_xyhbond_nbd_refined0.227
r_xyhbond_nbd_refined0.209
r_symmetry_nbd_other0.198
r_nbtor_refined0.176
r_chiral_restr0.119
r_metal_ion_refined0.093
r_symmetry_nbtor_other0.085
r_symmetry_metal_ion_refined0.053
r_bond_refined_d0.019
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3804
Nucleic Acid Atoms
Solvent Atoms464
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling