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Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) NADP holoenzyme, from Helicobacter pylori, with active site cysteine oxidised to sulfenic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.2M NH4SO4,
0.1M Tris pH 8.5,
25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.7 54.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.478 α = 90 b = 96.196 β = 90 c = 94.728 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 16M 2023-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.2 38.362 98.8 0.089 1 22.2 23.9 120012
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 87.7 0.737 0.896 2.9 10.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.2 38.362 120008 5943 98.745 0.121 0.1204 0.1192 0.1366 0.1361 12.603
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] -0.78 0.307 0.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.275 r_lrange_it 14.45 r_lrange_other 12.951 r_dihedral_angle_3_deg 10.955 r_scangle_it 9.487 r_scangle_other 9.426 r_dihedral_angle_2_deg 8.962 r_dihedral_angle_1_deg 7.067 r_scbond_it 6.814 r_scbond_other 6.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.275 r_lrange_it 14.45 r_lrange_other 12.951 r_dihedral_angle_3_deg 10.955 r_scangle_it 9.487 r_scangle_other 9.426 r_dihedral_angle_2_deg 8.962 r_dihedral_angle_1_deg 7.067 r_scbond_it 6.814 r_scbond_other 6.755 r_mcangle_other 5.543 r_mcangle_it 5.526 r_rigid_bond_restr 4.647 r_mcbond_it 3.936 r_mcbond_other 3.862 r_angle_refined_deg 1.963 r_dihedral_angle_other_2_deg 1.936 r_angle_other_deg 0.707 r_nbd_refined 0.226 r_symmetry_nbd_refined 0.21 r_symmetry_nbd_other 0.194 r_symmetry_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.172 r_nbd_other 0.148 r_chiral_restr 0.137 r_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2534 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement xia2.multiplex data reduction xia2.multiplex data scaling MoRDa phasing