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Sucrose-phosphate synthase-like protein from Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8UAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 26% PEG 3350, 200 mM Magnesium Chloride, 1mM UDPG, Protein crystal seeds
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.057 α = 90 b = 92.709 β = 120.44 c = 100.55 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 EIGER X 16M 2023-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953733 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.74 48.05 99 0.052 0.062 0.033 0.999 13.8 3.5 104260 21.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 95.8 0.612 0.722 0.379 0.705 2.1 3.5
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 1.74 48.08 98986 5262 98.86 0.1807 0.17904 0.1881 0.21102 0.2143 RANDOM 23.921
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] -0.86 -0.14 1.44 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.83 r_dihedral_angle_2_deg 7.938 r_dihedral_angle_1_deg 6.5 r_long_range_B_refined 5.734 r_long_range_B_other 5.733 r_scangle_other 4.698 r_scbond_it 3.071 r_scbond_other 3.07 r_mcangle_other 2.959 r_mcangle_it 2.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.83 r_dihedral_angle_2_deg 7.938 r_dihedral_angle_1_deg 6.5 r_long_range_B_refined 5.734 r_long_range_B_other 5.733 r_scangle_other 4.698 r_scbond_it 3.071 r_scbond_other 3.07 r_mcangle_other 2.959 r_mcangle_it 2.958 r_mcbond_it 2.173 r_mcbond_other 2.165 r_angle_refined_deg 1.637 r_angle_other_deg 0.591 r_chiral_restr 0.088 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 7268 Nucleic Acid Atoms Solvent Atoms 646 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing