8QD8

Wdyg1p in complex with 1,3-Dihydroxynaphthalene


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 DROP8.7293100 mM tris pH 8.7, 24% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3848.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.8α = 90
b = 88.85β = 90
c = 123.05γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-09-20MSINGLE 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
11.655098.70.05811.84.4111963
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)
11.651.7598.40.6522.1

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 REPLACEMENTTHROUGHOUT1.6543.57106353559898.690.164690.163460.18807RANDOM29.512
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]
1.999.47-11.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.242
r_dihedral_angle_4_deg14.6
r_dihedral_angle_3_deg11.841
r_dihedral_angle_1_deg6.096
r_long_range_B_refined1.715
r_long_range_B_other1.715
r_angle_other_deg1.174
r_angle_refined_deg1.16
r_scangle_other0.971
r_mcangle_it0.915
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.242
r_dihedral_angle_4_deg14.6
r_dihedral_angle_3_deg11.841
r_dihedral_angle_1_deg6.096
r_long_range_B_refined1.715
r_long_range_B_other1.715
r_angle_other_deg1.174
r_angle_refined_deg1.16
r_scangle_other0.971
r_mcangle_it0.915
r_mcangle_other0.915
r_scbond_it0.762
r_scbond_other0.762
r_mcbond_it0.706
r_mcbond_other0.704
r_rigid_bond_restr0.482
r_chiral_restr0.055
r_bond_refined_d0.003
r_gen_planes_refined0.003
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 Atoms6604
Nucleic Acid Atoms
Solvent Atoms757
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing