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K403 acetylated glucose-6-phosphate dehydrogenase (G6PD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QKI 1QKI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 5% Tacsimate,
0.1M Hepes pH 7.0
10% PEG MME 5000
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.363 α = 77.23 b = 122.609 β = 80.99 c = 161.31 γ = 77.4
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 X 16M 2021-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.28 117.38 97 0.112 0.992 5 6.5 205547
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.32 0.313
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1QKI 2.28 50.01 195116 10329 96.94 0.21319 0.21068 0.2188 0.26098 0.2623 RANDOM 55.981
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] -0.24 0.02 -0.15 0.76 -0.96 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.022 r_dihedral_angle_3_deg 19.372 r_long_range_B_other 10.788 r_long_range_B_refined 10.785 r_scangle_other 9.053 r_dihedral_angle_1_deg 7.233 r_mcangle_it 7.229 r_mcangle_other 7.229 r_scbond_it 6.598 r_scbond_other 6.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.022 r_dihedral_angle_3_deg 19.372 r_long_range_B_other 10.788 r_long_range_B_refined 10.785 r_scangle_other 9.053 r_dihedral_angle_1_deg 7.233 r_mcangle_it 7.229 r_mcangle_other 7.229 r_scbond_it 6.598 r_scbond_other 6.598 r_mcbond_it 5.251 r_mcbond_other 5.251 r_angle_refined_deg 2.049 r_angle_other_deg 0.695 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32357 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing