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Crystal structure of the C-terminally truncated human E574Q-PGGHG mutant in complex with glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9SD4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.7 289 Ratio: 1:1
Co-crystallized with 10mM KJB
Conditions: 20% PEG 3350, 0.1 M Tris pH 8.7, 0.2 M NaCl.
Crystal Properties Matthews coefficient Solvent content 2.17 43.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.071 α = 90 b = 77.076 β = 98.552 c = 79.888 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2021-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
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 1.36 79 99.9 0.027 0.999 20.2 6.6 137926 12.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.39 99.9 0.296 0.757 3.4 5.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.363 79 137898 6965 99.929 0.137 0.1357 0.1357 0.1573 0.1573 RANDOM 14.084
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 0.374 -0.372 0.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.226 r_dihedral_angle_3_deg 11.611 r_dihedral_angle_2_deg 9.991 r_dihedral_angle_1_deg 6.957 r_lrange_it 5.763 r_lrange_other 5.763 r_scangle_it 4.256 r_scangle_other 4.256 r_scbond_it 2.869 r_scbond_other 2.868
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.226 r_dihedral_angle_3_deg 11.611 r_dihedral_angle_2_deg 9.991 r_dihedral_angle_1_deg 6.957 r_lrange_it 5.763 r_lrange_other 5.763 r_scangle_it 4.256 r_scangle_other 4.256 r_scbond_it 2.869 r_scbond_other 2.868 r_mcangle_it 2.307 r_mcangle_other 2.307 r_angle_refined_deg 2.021 r_mcbond_it 1.581 r_mcbond_other 1.574 r_angle_other_deg 0.69 r_symmetry_xyhbond_nbd_refined 0.248 r_nbd_refined 0.226 r_symmetry_nbd_refined 0.219 r_nbd_other 0.211 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.108 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5322 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 129
Software Software Software Name Purpose autoPROC data processing Aimless data scaling MOLREP phasing REFMAC refinement Coot model building