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Glucose-6-phosphate dehydrogenase from Leishmania donovani in complex with 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 2.36 50.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 193.396 α = 90 b = 92.381 β = 94.435 c = 70.628 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 2022-11-14 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 2.3 29.554 99.6 0.99 6.3 7.4 54957
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 2.3 9.76 0.937 8
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 2.3 29.554 54760 2753 99.25 0.232 0.2278 0.2311 0.3142 0.3162 28.218
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] -0.792 -1.254 1.989 -0.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.488 r_dihedral_angle_6_deg 13.868 r_dihedral_angle_2_deg 9.42 r_dihedral_angle_1_deg 6.868 r_lrange_it 6.24 r_lrange_other 6.214 r_scangle_it 4.244 r_scangle_other 4.243 r_mcangle_it 3.586 r_mcangle_other 3.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.488 r_dihedral_angle_6_deg 13.868 r_dihedral_angle_2_deg 9.42 r_dihedral_angle_1_deg 6.868 r_lrange_it 6.24 r_lrange_other 6.214 r_scangle_it 4.244 r_scangle_other 4.243 r_mcangle_it 3.586 r_mcangle_other 3.586 r_scbond_it 2.587 r_scbond_other 2.587 r_mcbond_it 2.268 r_mcbond_other 2.268 r_angle_refined_deg 1.284 r_angle_other_deg 0.438 r_nbd_other 0.252 r_nbd_refined 0.211 r_symmetry_nbd_other 0.208 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_refined 0.192 r_nbtor_refined 0.179 r_symmetry_xyhbond_nbd_refined 0.178 r_symmetry_xyhbond_nbd_other 0.162 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8137 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing