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Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD (P1 form2)
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 6.5 291 Morpheus Fusion, B4 : 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic dihydrate, 20 mM Potassium sodium tartrate tetrahydrate, 20 mM Sodium oxamate, 0.12 M Ethyleneglycol 40 mM Imidazole, 60 mM MES monohydrate (acid), pH 6.5, 20% v/v PEG 500 MME, 10 % w/v PEG 20000, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD, plate 20064 B4 drop 1, Puck: PSL-2206, Cryo: direct
Crystal Properties Matthews coefficient Solvent content 3.13 60.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.358 α = 76.3 b = 139.715 β = 87.32 c = 222.702 γ = 88.12
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 2025-06-28 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 3.09 48.29 97.5 0.102 0.121 0.064 0.995 10 3.5 159633
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 3.09 3.17 97.7 1.004 1.175 0.606 0.689 3.7
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 3.09 48.29 1.96 159519 7914 97.5 0.1834 0.1809 0.1827 0.2335 0.2314
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 14.397 f_angle_d 0.766 f_chiral_restr 0.049 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 49281 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 576
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction