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Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with pseudo substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AQ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 4% Tacsimate, 12% PEG3350, 4-8% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.49 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.84 α = 90 b = 97.685 β = 94.005 c = 70.449 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 RIGAKU HyPix-6000HE 2023-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.25 30.195 99.8 0.96 6 6.7 61443
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.31 100 0.917 7.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.25 30.195 61423 3091 99.698 0.223 0.2196 0.223 0.2863 0.2906 22.543
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] -0.468 -0.846 1.276 -0.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.083 r_dihedral_angle_6_deg 14.673 r_dihedral_angle_2_deg 9.688 r_dihedral_angle_1_deg 7.101 r_lrange_it 5.907 r_lrange_other 5.846 r_scangle_it 3.617 r_scangle_other 3.616 r_mcangle_it 3.171 r_mcangle_other 3.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.083 r_dihedral_angle_6_deg 14.673 r_dihedral_angle_2_deg 9.688 r_dihedral_angle_1_deg 7.101 r_lrange_it 5.907 r_lrange_other 5.846 r_scangle_it 3.617 r_scangle_other 3.616 r_mcangle_it 3.171 r_mcangle_other 3.171 r_scbond_it 2.181 r_scbond_other 2.181 r_mcbond_it 1.942 r_mcbond_other 1.942 r_angle_refined_deg 1.32 r_angle_other_deg 0.475 r_chiral_restr_other 0.313 r_symmetry_nbd_refined 0.228 r_nbd_other 0.226 r_nbd_refined 0.218 r_symmetry_nbd_other 0.21 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.17 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.064 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8040 Nucleic Acid Atoms Solvent Atoms 724 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing