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Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) apoenzyme, from Helicobacter pylori
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 6.5 291 0.2M NH4SO4,
0.1M Bis-Tris pH 6.5,
25% w/v PEG3350
300nl drop, mixed either 1:1 or 2:1
Crystal Properties Matthews coefficient Solvent content 2.82 56.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.938 α = 90 b = 94.811 β = 90 c = 95.726 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 1.44 67.36 95.4 0.088 0.999 16.6 13.7 55539
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 1.44 1.57 69.3 1.838 0.741 13.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.444 67.36 55539 2795 77.25 0.142 0.1403 0.1767 0.1773 18.895
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] -2.609 3.276 -0.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.106 r_dihedral_angle_3_deg 13.302 r_dihedral_angle_2_deg 12.601 r_dihedral_angle_1_deg 6.99 r_rigid_bond_restr 5.652 r_lrange_it 3.782 r_lrange_other 3.587 r_scangle_it 2.936 r_scangle_other 2.874 r_scbond_it 2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.106 r_dihedral_angle_3_deg 13.302 r_dihedral_angle_2_deg 12.601 r_dihedral_angle_1_deg 6.99 r_rigid_bond_restr 5.652 r_lrange_it 3.782 r_lrange_other 3.587 r_scangle_it 2.936 r_scangle_other 2.874 r_scbond_it 2.14 r_scbond_other 2.109 r_mcangle_it 2.101 r_mcangle_other 2.101 r_angle_refined_deg 1.769 r_mcbond_it 1.483 r_mcbond_other 1.475 r_angle_other_deg 0.624 r_nbd_refined 0.218 r_symmetry_nbd_other 0.206 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.164 r_nbd_other 0.152 r_symmetry_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.122 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2476 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MoRDa phasing