☰ Navigation Tabs
The crystal structure of the post-reactive state of UDP-sugar pyrophosphorylase from Leishmania major in complex with product UDP-Glucose and by-product analog VO4 (orthovanadate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 200 mM ammonium acetate, 100 mM tri-sodium citrate, pH 5.4 - 5.6, and 15% - 17% polyethylene glycol-4000 (PEG-4000)
Crystal Properties Matthews coefficient Solvent content 2.83 56.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.08 α = 90 b = 122.42 β = 105.55 c = 61.24 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 PIXEL DECTRIS PILATUS 6M 2018-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 2.2 59.1 99.9 0.048 0.0339 0.999 15.41 6.9 38888 70.626
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 99.8 0.5922 0.4284 0.85 2.18 7.04
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.2 59.07 36921 1967 99.93 0.21275 0.21111 0.2169 0.24221 0.2414 RANDOM 68.667
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] -0.99 -2.35 -0.74 2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.996 r_dihedral_angle_3_deg 15.263 r_dihedral_angle_4_deg 14.749 r_long_range_B_refined 8.905 r_long_range_B_other 8.898 r_mcangle_it 6.458 r_mcangle_other 6.457 r_scangle_other 6.338 r_dihedral_angle_1_deg 5.397 r_scbond_it 4.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.996 r_dihedral_angle_3_deg 15.263 r_dihedral_angle_4_deg 14.749 r_long_range_B_refined 8.905 r_long_range_B_other 8.898 r_mcangle_it 6.458 r_mcangle_other 6.457 r_scangle_other 6.338 r_dihedral_angle_1_deg 5.397 r_scbond_it 4.708 r_scbond_other 4.656 r_mcbond_it 4.645 r_mcbond_other 4.645 r_angle_other_deg 2.237 r_angle_refined_deg 1.262 r_chiral_restr 0.061 r_bond_other_d 0.035 r_gen_planes_other 0.023 r_gen_planes_refined 0.011 r_bond_refined_d 0.008 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 Atoms Number Protein Atoms 4706 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction SADABS data scaling PHASER phasing