8ZI6 | pdb_00008zi6

Crystal structure of SrUGT76G4 in complex with UDP-glucose


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
2.1241.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.78α = 90
b = 111.78β = 90
c = 91.77γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 S 9M2023-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.97918SSRFBL02U1

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
12.833.9996.10.2480.2670.0940.9715.46.930343
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)
12.82.9586.30.9121.0030.3970.5545.1

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 REPLACEMENTTHROUGHOUT2.833.9928750156095.980.272440.268060.27020.351220.3499RANDOM55.168
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]
0.270.130.27-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.263
r_long_range_B_refined9.165
r_long_range_B_other9.164
r_dihedral_angle_1_deg8.477
r_dihedral_angle_2_deg6.362
r_mcangle_it6.04
r_mcangle_other6.039
r_scangle_other5.234
r_mcbond_it3.675
r_mcbond_other3.675
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.263
r_long_range_B_refined9.165
r_long_range_B_other9.164
r_dihedral_angle_1_deg8.477
r_dihedral_angle_2_deg6.362
r_mcangle_it6.04
r_mcangle_other6.039
r_scangle_other5.234
r_mcbond_it3.675
r_mcbond_other3.675
r_scbond_it3.101
r_scbond_other3.1
r_angle_refined_deg1.325
r_angle_other_deg0.459
r_chiral_restr0.06
r_bond_refined_d0.004
r_gen_planes_refined0.004
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 Atoms9354
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing