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Glucose-6-phosphate dehydrogenase from Leishmania donovani
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 2.45 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.327 α = 90 b = 97.356 β = 93.829 c = 70.346 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 4M 2023-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.968 ESRF MASSIF-3
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 2.4 54.886 98.9 0.978 6.8 4.8 49811
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 2.4 9.6 0.826 4.9
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 2.4 54.886 49803 2525 98.774 0.2 0.1967 0.1998 0.2593 0.2624 40.975
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] -2.255 -3.233 2.106 0.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.055 r_dihedral_angle_3_deg 14.836 r_dihedral_angle_2_deg 7.971 r_lrange_it 7.288 r_lrange_other 7.277 r_dihedral_angle_1_deg 7.092 r_scangle_it 5.347 r_scangle_other 5.346 r_mcangle_it 4.926 r_mcangle_other 4.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.055 r_dihedral_angle_3_deg 14.836 r_dihedral_angle_2_deg 7.971 r_lrange_it 7.288 r_lrange_other 7.277 r_dihedral_angle_1_deg 7.092 r_scangle_it 5.347 r_scangle_other 5.346 r_mcangle_it 4.926 r_mcangle_other 4.926 r_scbond_it 3.387 r_scbond_other 3.387 r_mcbond_it 3.185 r_mcbond_other 3.179 r_angle_refined_deg 1.247 r_angle_other_deg 0.435 r_symmetry_xyhbond_nbd_refined 0.283 r_nbd_other 0.232 r_nbd_refined 0.216 r_symmetry_nbd_other 0.207 r_symmetry_nbd_refined 0.197 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.172 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_symmetry_xyhbond_nbd_other 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8026 Nucleic Acid Atoms Solvent Atoms 364 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing