5A4W

AtGSTF2 from Arabidopsis thaliana in complex with quercetrin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

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

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.35α = 90
b = 93.57β = 90
c = 152.42γ = 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
12.2559.091000.0916.56.8600222
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)
12.252.311000.723.27.1

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 1GNW2.2559.0957023293599.950.208950.207240.24195RANDOM38.915
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]
-1.085.17-4.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.105
r_dihedral_angle_4_deg18.238
r_dihedral_angle_3_deg14.155
r_dihedral_angle_1_deg6.32
r_mcangle_it4.399
r_scbond_it3.4
r_mcbond_it3.01
r_mcbond_other3.01
r_angle_refined_deg1.73
r_angle_other_deg1.649
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.105
r_dihedral_angle_4_deg18.238
r_dihedral_angle_3_deg14.155
r_dihedral_angle_1_deg6.32
r_mcangle_it4.399
r_scbond_it3.4
r_mcbond_it3.01
r_mcbond_other3.01
r_angle_refined_deg1.73
r_angle_other_deg1.649
r_chiral_restr0.093
r_bond_refined_d0.013
r_bond_other_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.009
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 Atoms9778
Nucleic Acid Atoms
Solvent Atoms325
Heterogen Atoms270

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing