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Natural product inhibitor of glyceraldehyde-3-phosphate dehydrogenase(GAPDH)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Sodium acetate, 0.1M HEPES-NaOH pH7.5, 22%(W/V) PEG4000, 4.4%(V/V) Formamide
Crystal Properties Matthews coefficient Solvent content 2.42 49.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.235 α = 90 b = 125.934 β = 90 c = 132.097 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 195 PIXEL DECTRIS PILATUS3 X CdTe 1M 2025-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 62.967 99.4 0.125 0.253 0.986 2.77 10.6 85324
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 64.7 27.25
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1U8F 1.87 62.967 1.33 71022 1864 60.29 0.2137 0.2119 0.2199 0.2819 0.2846
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 f_dihedral_angle_d 14.492 f_angle_d 1.345 f_chiral_restr 0.066 f_bond_d 0.015 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10293 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PDB_EXTRACT data extraction PHASER phasing