2CNB

Trypanosoma brucei UDP-galactose-4-epimerase in ternary complex with NAD and the substrate analogue UDP-4-deoxy-4-fluoro-alpha-D-galactose


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
188% PEG 8000, 200MM KCL, 50MM NA2B4O7, 5% GLYCEROL, PH 8.5
Crystal Properties
Matthews coefficientSolvent content
358.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.724α = 90
b = 111.694β = 90
c = 160.873γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORS2005-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.79296.80.0915.24.549501264.7
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)
12.72.7778.90.472.43.3

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONOTHERTHROUGHOUT2.791.6748640245495.30.2030.1990.281RANDOM48.29
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]
3.4810.428-3.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.012
r_dihedral_angle_3_deg17.99
r_dihedral_angle_4_deg17.617
r_dihedral_angle_1_deg6.206
r_scangle_it2.266
r_angle_refined_deg1.464
r_scbond_it1.439
r_mcangle_it1.135
r_mcbond_it0.624
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.012
r_dihedral_angle_3_deg17.99
r_dihedral_angle_4_deg17.617
r_dihedral_angle_1_deg6.206
r_scangle_it2.266
r_angle_refined_deg1.464
r_scbond_it1.439
r_mcangle_it1.135
r_mcbond_it0.624
r_nbtor_refined0.314
r_symmetry_vdw_refined0.226
r_nbd_refined0.22
r_symmetry_hbond_refined0.187
r_xyhbond_nbd_refined0.171
r_chiral_restr0.099
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms11348
Nucleic Acid Atoms
Solvent Atoms416
Heterogen Atoms320

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling