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Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase from Bordetella pertussis (Apo, trigonal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9PG6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Index H1: 100 mM Tris, pH 8.5, 200 mM MgCl2, 25% (w/v) PEG 3350. BopeA.00052.a.B2.PW39379 at 12.4 mg/mL. 5mM NAD and D-glyceraldehyde-3-phosphate added to the protein prior to crystallization but no electron density for the ligands was observed. plate 19840 well H1 drop 3 , Puck: PSL-2105, Cryo: 80% crystallant + 20% PEG 200
Crystal Properties Matthews coefficient Solvent content 2.24 44.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.461 α = 90 b = 83.461 β = 90 c = 166.173 γ = 120
Symmetry Space Group P 31 2 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 2025-04-25 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 1.5 43.97 100 0.108 0.111 0.025 1 17.7 20.2 107896
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 1.5 1.53 100 2.386 2.445 0.533 0.376 20.9
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 1.5 43.97 1.34 107818 5393 99.99 0.1636 0.1625 0.1702 0.1856 0.1919
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 15.105 f_angle_d 1.057 f_chiral_restr 0.062 f_plane_restr 0.011 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5044 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction