1UQT

Trehalose-6-phosphate from E. coli bound with UDP-2-fluoro glucose.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GZ5PDB ENTRY 1GZ5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1830% PEG 4000, 200MM AMMONIUM ACETATE, 100MM TRISHCL PH 8
Crystal Properties
Matthews coefficientSolvent content
2.449.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.919α = 90
b = 101.521β = 90
c = 118.207γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRFESRFID14-2

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
122097.80.06118.73.767542
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)
122.0783.80.4552.332.66

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 1GZ5219.9267541359497.70.220.2190.251RANDOM20.62
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]
-0.24-0.090.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.32
r_scangle_it2.944
r_scbond_it1.867
r_angle_refined_deg1.558
r_mcangle_it1.127
r_angle_other_deg1.01
r_mcbond_it0.615
r_symmetry_vdw_other0.296
r_symmetry_vdw_refined0.246
r_nbd_other0.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.32
r_scangle_it2.944
r_scbond_it1.867
r_angle_refined_deg1.558
r_mcangle_it1.127
r_angle_other_deg1.01
r_mcbond_it0.615
r_symmetry_vdw_other0.296
r_symmetry_vdw_refined0.246
r_nbd_other0.237
r_nbd_refined0.215
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.165
r_chiral_restr0.121
r_nbtor_other0.091
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms7236
Nucleic Acid Atoms
Solvent Atoms103
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing