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Crystal Structure of UDP-glucose phosphorylase from Trypanosoma Brucei, (Tb10.389.0330)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OEG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 22% PEG3350, 0.1M Ammonium sulfate, 0.1M Bis Tris, 18% glycerol, 2 mM UDP-glucose, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.697 α = 90 b = 77.485 β = 117.88 c = 112.209 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2009-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.92 50 98.7 0.121 0.096 10.452 3.1 97362 96096 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.99 90.6 0.707 0.645 1.33 3 8757
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2oeg 1.92 25 97332 96067 4791 98.7 0.243 0.243 0.241 0.2387 0.294 0.2923 RANDOM 28.157
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] -0.77 0.45 0.28 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.928 r_dihedral_angle_3_deg 16.275 r_dihedral_angle_4_deg 14.535 r_dihedral_angle_1_deg 6.343 r_scangle_it 2.401 r_scbond_it 1.693 r_angle_refined_deg 1.519 r_mcangle_it 0.972 r_mcbond_it 0.633 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.928 r_dihedral_angle_3_deg 16.275 r_dihedral_angle_4_deg 14.535 r_dihedral_angle_1_deg 6.343 r_scangle_it 2.401 r_scbond_it 1.693 r_angle_refined_deg 1.519 r_mcangle_it 0.972 r_mcbond_it 0.633 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.18 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7235 Nucleic Acid Atoms Solvent Atoms 733 Heterogen Atoms 158
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction BALBES phasing