5OEU

The structure of a glutathione synthetase like-effector (GSS22) from Globodera pallida in ADP-bound closed conformation.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OEV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9293.150.2 M tri-methylamine N-oxide, 0.1 M Tris pH 9 and 20 % w/v PEG 2000 MME with the addition of ADP (2.5 mM), MgCl2 (5 mM) and GSH (2.5 mM)
Crystal Properties
Matthews coefficientSolvent content
2.8657.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.27α = 90
b = 121.079β = 90
c = 128.338γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.98DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.57501000.1470.15413.711.139223
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.711.3481.14

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT5OEV2.575038293206899.960.2170.21530.2474RANDOM53.378
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]
0.51-1.090.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.142
r_dihedral_angle_3_deg15.619
r_dihedral_angle_4_deg13.248
r_dihedral_angle_1_deg6.067
r_angle_refined_deg1.394
r_angle_other_deg0.917
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.142
r_dihedral_angle_3_deg15.619
r_dihedral_angle_4_deg13.248
r_dihedral_angle_1_deg6.067
r_angle_refined_deg1.394
r_angle_other_deg0.917
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6936
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data processing
xia2data reduction
MOLREPphasing