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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Neisseria gonorrhoeae in complex with NAD (Orthorhombic I form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 Berkeley D4: 25% (w/v) PEG 3350, 100 mM sodium acetate pH 4.5. 2mM NAD addied prior to crystallization, plate 20205 well D4 drop 3 , Puck: PSL2003, Cryo: 80% crystallant + 20% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.4 48.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.189 α = 90 b = 123.985 β = 90 c = 130.745 γ = 90
Symmetry Space Group I 2 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 EIGER2 XE 9M 2025-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.9 48.19 100 0.069 0.072 0.02 1 18.9 13.3 56062
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 1.743 1.813 0.495 0.748 13.3
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 FREE R-VALUE 1.9 48.19 1.34 56044 2808 99.96 0.1769 0.175 0.1795 0.2144 0.2156
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 17.838 f_angle_d 1.131 f_chiral_restr 0.065 f_plane_restr 0.013 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4699 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction