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Glyceraldehyde 3-phosphate dehydrogenase A (GAPDHA) NAD holoenzyme, from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 200mM sodium citrate tribasic
20% PEG 3350 (w/v)
solution was mixed 4:1:1 or 3:2:1 (protein: reservoir: seeds) in 300nl drops.
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.936 α = 90 b = 94.866 β = 90 c = 95.701 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 2023-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.6888 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 1.16 67.37 94.1 0.13 0.997 11.3 13.8 82091
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 1.16 1.31 62.4 1.703 0.833 1.6 13.4
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 1.162 67.37 82089 4194 61.302 0.138 0.1364 0.1368 0.1637 0.1646 13.238
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] -2.003 2.154 -0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.602 r_lrange_it 15.107 r_lrange_other 13.858 r_dihedral_angle_3_deg 11.376 r_dihedral_angle_2_deg 9.62 r_scangle_it 8.327 r_scangle_other 8.178 r_dihedral_angle_1_deg 7.122 r_scbond_it 5.946 r_scbond_other 5.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.602 r_lrange_it 15.107 r_lrange_other 13.858 r_dihedral_angle_3_deg 11.376 r_dihedral_angle_2_deg 9.62 r_scangle_it 8.327 r_scangle_other 8.178 r_dihedral_angle_1_deg 7.122 r_scbond_it 5.946 r_scbond_other 5.727 r_mcangle_other 5.202 r_mcangle_it 5.195 r_rigid_bond_restr 4.95 r_mcbond_it 3.557 r_mcbond_other 3.52 r_angle_refined_deg 1.989 r_angle_other_deg 0.843 r_nbd_refined 0.218 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.164 r_nbd_other 0.15 r_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_nbd_refined 0.127 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.075 r_dihedral_angle_other_2_deg 0.071 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2534 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling PHASER phasing