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Crystal structure of UDP-glucose pyrophosphorylase V402W mutant from Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 2.25M ammonium sulfate, 100mM Tris-HCl pH 7.2, 0.1% Tween 80
Crystal Properties Matthews coefficient Solvent content 2.65 53.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.56 α = 90 b = 70.89 β = 123.54 c = 112.29 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 2015-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.9 47.854 99.9 0.0183 4.37 7.04 26339 21.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2OEF 2.9 47.854 1.33 26290 1396 99.74 0.228 0.2256 0.2232 0.2694 0.2671
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.611 f_angle_d 0.876 f_chiral_restr 0.062 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7465 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction SADABS data scaling AMoRE phasing