8QD9

Wdyg1p in complex with 1,3,6,8-Tetrahydroxynaphthalene


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8QD1Ayg1p from A. fumigatus catalyzes polyketide shortening in the biosynthesis of DHN-melanin

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293100 mM tris pH 8.5, 21% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.22α = 90
b = 88.49β = 90
c = 122.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.955098.50.06214.14.567832
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0596.40.6382.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9543.4664426339198.480.16030.158040.20337RANDOM36.131
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]
21.62-22.080.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.437
r_dihedral_angle_4_deg14.741
r_dihedral_angle_3_deg12.205
r_dihedral_angle_1_deg6.351
r_long_range_B_refined2.588
r_long_range_B_other2.466
r_mcangle_it1.714
r_mcangle_other1.714
r_scangle_other1.713
r_scbond_it1.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.437
r_dihedral_angle_4_deg14.741
r_dihedral_angle_3_deg12.205
r_dihedral_angle_1_deg6.351
r_long_range_B_refined2.588
r_long_range_B_other2.466
r_mcangle_it1.714
r_mcangle_other1.714
r_scangle_other1.713
r_scbond_it1.308
r_scbond_other1.308
r_mcbond_it1.297
r_mcbond_other1.296
r_angle_refined_deg1.204
r_angle_other_deg1.181
r_rigid_bond_restr0.679
r_chiral_restr0.057
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6521
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing