6YGF

NADase from Aspergillus fumigatus with trapped reaction products


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YGED_1292105770

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.04 M Potassium phosphate monobasic, 16% PEG 8000 and 20% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.957.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.815α = 90
b = 63.815β = 90
c = 257.723γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.03320PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.785.999.740.024650.99915.1726823627.48
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.760.6440.4771.04

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUED_12921057701.785.91.3468230338799.750.17080.16920.201335.24
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.9506
f_angle_d0.8805
f_chiral_restr0.0553
f_bond_d0.0068
f_plane_restr0.0067
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3302
Nucleic Acid Atoms
Solvent Atoms559
Heterogen Atoms263

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction