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Crystal structure of C-terminally truncated human PGGHG 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 8 289 Precipitant ratio 1:1
Co-crystallized 5% (0.27 mM) Glucose.
Condition: 20% PEG 8K, 0.05 M KPO4
Crystal Properties Matthews coefficient Solvent content 2.2 44.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.323 α = 90 b = 75.891 β = 90 c = 318.908 γ = 90
Symmetry Space Group P 21 21 21
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 2021-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 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 1.61 159.454 99.98 0.027 0.9977 12.637 12.71 1747763 27.7
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 1.61 1.638 99.88 0.566 0.6222 1.158 10.42
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 (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 1.61 159.45 166028 8735 99.91 0.17557 0.17379 0.1844 0.20937 0.2193 RANDOM 37.22
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] 2.35 -2.02 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.77 r_dihedral_angle_2_deg 11.778 r_dihedral_angle_1_deg 8.517 r_long_range_B_refined 6.855 r_long_range_B_other 6.828 r_scangle_other 5.277 r_mcangle_other 3.567 r_mcangle_it 3.566 r_scbond_it 3.48 r_scbond_other 3.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.77 r_dihedral_angle_2_deg 11.778 r_dihedral_angle_1_deg 8.517 r_long_range_B_refined 6.855 r_long_range_B_other 6.828 r_scangle_other 5.277 r_mcangle_other 3.567 r_mcangle_it 3.566 r_scbond_it 3.48 r_scbond_other 3.48 r_mcbond_it 2.536 r_mcbond_other 2.534 r_angle_refined_deg 1.708 r_angle_other_deg 0.599 r_chiral_restr 0.088 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 10587 Nucleic Acid Atoms Solvent Atoms 794 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement autoPROC data processing MOLREP phasing Coot model building autoPROC data reduction autoPROC data scaling PDB_EXTRACT data extraction