6YZZ

Arabidopsis thaliana Naa50 in complex with AcCoA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5291.1534 mg mL-1 protein (20 mM HEPES pH 8.0, 250 mM NaCl) mixed with AcCoA (5.4 mM); drops (600 nL): 1:1 mix of (20 mM HEPES pH 8.0, 250 mM NaCl) and (0.9 M sodium citrate, 0.1 M sodium cacodylate pH 6.5). Growth after 19 h, 20 % glycerol (v/v) as cryo protection
Crystal Properties
Matthews coefficientSolvent content
2.1643.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.164α = 90
b = 100.164β = 90
c = 100.164γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.0781ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim 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
11.7940.891000.019121.27.51604633.54
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.821000.7520.61617.6

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-VALUE2ob01.7940.891.341603685299.890.17130.16990.19743.85
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_d16.6939
f_angle_d0.9212
f_chiral_restr0.0572
f_bond_d0.0069
f_plane_restr0.0042
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1207
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms51

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing
PHENIXrefinement