5OET

The structure of a glutathione synthetase like-effector (GSS30) from Globodera pallida in apoform.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.2 M magnesium formate di-hydrate and 20 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4449.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.75α = 90
b = 81.619β = 103.18
c = 93.84γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-05-15MSINGLE 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
12.575099.70.1360.1498.75.732990
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)
12.62.720.9971.097

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 REPLACEMENTTHROUGHOUT5OEV2.575032399166199.840.25290.25130.2852RANDOM56.711
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]
-4.78-0.94.670.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.976
r_dihedral_angle_4_deg18.581
r_dihedral_angle_3_deg17.791
r_dihedral_angle_1_deg6.932
r_angle_refined_deg1.482
r_angle_other_deg0.933
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.976
r_dihedral_angle_4_deg18.581
r_dihedral_angle_3_deg17.791
r_dihedral_angle_1_deg6.932
r_angle_refined_deg1.482
r_angle_other_deg0.933
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6693
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data processing
xia2data reduction
MOLREPphasing