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Crystal structure of a glyceraldehyde-3-phosphate dehydrogenase from Neisseria gonorrhoeae in complex with NAD and GLYCERALDEHYDE-3-PHOSPHATE
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 7.5 291 Berkeley H9: 25% PEG 4000, 0.10M HEPES pH 7.5, 10% iso-Propanol. NegoA.00617.a.B1.PS38018 at 8 mg/mL. cocrystallization with NAD and G3H, plate 20061 H9 drop 1, Puck: PSL-2203, Cryo: 80% crystallant + 20% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.06 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.647 α = 90 b = 105.543 β = 94.63 c = 167.699 γ = 90
Symmetry Space Group P 1 21 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 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 1.91 49.27 99.9 0.178 0.192 0.073 0.996 9.8 6.9 184320
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 1.91 1.96 100 1.309 1.413 0.527 0.581 7.1
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 1.91 48.89 1.35 184233 9113 99.9 0.1563 0.1547 0.1663 0.187 0.1955
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 13.993 f_angle_d 1.031 f_chiral_restr 0.059 f_plane_restr 0.012 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20011 Nucleic Acid Atoms Solvent Atoms 1298 Heterogen Atoms 549
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction