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UDP-Glucose Pyrophosphorylase from Leishmania major in complex with UTP analog dUpCpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OEF pdb entry 2OEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293.15 0.1 M MES, 20% w/v PEG-4000, 200 mM Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K, pH 6.4
Crystal Properties Matthews coefficient Solvent content 2.67 53.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.25 α = 90 b = 108.47 β = 90 c = 152.59 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD monochromator (horizontally side diffracting Silicon 111 crystal). 2013-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
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 3 47.3 90 8 11.6 11 126117 11151 2 2 70
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 pdb entry 2OEF 3 47.27 11151 10539 546 90 0.21642 0.21642 0.21326 0.2126 0.27914 0.2842 RANDOM 84.193
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 r_dihedral_angle_2_deg 37.569 r_dihedral_angle_3_deg 16.49 r_dihedral_angle_4_deg 13.663 r_long_range_B_refined 11.401 r_long_range_B_other 11.295 r_scangle_other 8.208 r_mcangle_it 7.58 r_mcangle_other 7.578 r_scbond_it 5.382 r_scbond_other 5.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.569 r_dihedral_angle_3_deg 16.49 r_dihedral_angle_4_deg 13.663 r_long_range_B_refined 11.401 r_long_range_B_other 11.295 r_scangle_other 8.208 r_mcangle_it 7.58 r_mcangle_other 7.578 r_scbond_it 5.382 r_scbond_other 5.349 r_dihedral_angle_1_deg 5.203 r_mcbond_it 5.005 r_mcbond_other 5.005 r_angle_refined_deg 1.15 r_angle_other_deg 0.718 r_chiral_restr 0.056 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3730 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement CNS refinement MxCuBE data collection XDS data reduction SADABS data scaling CNS phasing