8ZI7 | pdb_00008zi7

Crystal structure of SrUGT76G4 in complex with Rubusoside


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelRobetta 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION5.52930.2 M NaSCN, 0.1 M NaCitrate pH5.5, 10-35% PEG3350, 8% D-Sorbitol
Crystal Properties
Matthews coefficientSolvent content
2.3647.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.026α = 90
b = 77.228β = 90
c = 86.134γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 9M2022-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.97914SSRFBL02U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.157.595.70.0850.0930.0360.997126.428050
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2299.90.9271.0010.3690.7566.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.157.526602138595.560.18530.18270.19160.2320.2346RANDOM54.002
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]
1.8-0.36-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.237
r_long_range_B_other11.374
r_long_range_B_refined11.372
r_dihedral_angle_2_deg8.862
r_scangle_other8.768
r_dihedral_angle_1_deg7.003
r_mcangle_other6.322
r_mcangle_it6.32
r_scbond_it5.661
r_scbond_other5.659
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.237
r_long_range_B_other11.374
r_long_range_B_refined11.372
r_dihedral_angle_2_deg8.862
r_scangle_other8.768
r_dihedral_angle_1_deg7.003
r_mcangle_other6.322
r_mcangle_it6.32
r_scbond_it5.661
r_scbond_other5.659
r_mcbond_it4.447
r_mcbond_other4.439
r_angle_refined_deg1.684
r_angle_other_deg0.565
r_chiral_restr0.08
r_gen_planes_refined0.007
r_bond_refined_d0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3238
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
autoPROCdata reduction
MOLREPphasing