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High Resolution Crystal Structure of Glyceraldehyde-3-Phosphate Dehydrogenase from Saccharomyces cerevisiae Complexed with a Maleate Derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 25% v/v PEG 3350, 0.2M Ammonium acetate, pH 6.3, 0.5M sodium chloride, 0.1M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.67 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.569 α = 90 b = 116.569 β = 90 c = 115.635 γ = 90
Symmetry Space Group I 41 2 2
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 2023-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.97918 SSRF BL10U2
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 1.95 82.43 99.87 0.994 8.97 21.5 29278
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 1.95 2.02 0.683
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 NONE 1.95 82.43 1.34 29261 1531 99.88 0.2105 0.2091 0.2107 0.2368 0.2336
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2450 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement DIALS data scaling XDS data reduction PHENIX phasing