5A4V

AtGSTF2 from Arabidopsis thaliana in complex with quercetin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GNWPDB ENTRY 1GNW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.1 M PTCP (PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE SYSTEM), 15% PEG 1.5K, PROTEIN AT 10 MG PER ML, pH 7
Crystal Properties
Matthews coefficientSolvent content
2.142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.03α = 90
b = 94.83β = 90
c = 153.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 2M2014-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

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
12.3859.0999.90.1114.96.7521582
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)
12.382.441000.682.87

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1GNW2.3859.5949588250699.90.204830.202860.24472RANDOM35.484
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]
-2.364.95-2.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.794
r_dihedral_angle_4_deg19.313
r_dihedral_angle_3_deg14.761
r_dihedral_angle_1_deg6.485
r_mcangle_it3.91
r_scbond_it3.015
r_mcbond_it2.64
r_mcbond_other2.637
r_angle_refined_deg1.685
r_angle_other_deg1.645
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.794
r_dihedral_angle_4_deg19.313
r_dihedral_angle_3_deg14.761
r_dihedral_angle_1_deg6.485
r_mcangle_it3.91
r_scbond_it3.015
r_mcbond_it2.64
r_mcbond_other2.637
r_angle_refined_deg1.685
r_angle_other_deg1.645
r_chiral_restr0.098
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.009
r_gen_planes_other0.008
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9868
Nucleic Acid Atoms
Solvent Atoms326
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing