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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 6.2 289 Precipitant ratio 1:1
Co-crystallized 5% (0.27 mM) Glucose.
Condition: 22.4% PEG 3350, 0.1 M Bis-Tris pH 6.2, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.14 42.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.021 α = 90 b = 77.382 β = 99.68 c = 78.814 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 2021-10-31 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 1.39 77.692 92.84 0.036 0.9979 11.003 6.32 105192 17.6
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 1.393 1.49 50.41 0.413 0.5655 1.244 4.46
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 1.39 77.69 99863 5329 82.43 0.15345 0.15204 0.1517 0.17997 0.1797 RANDOM 17.666
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] -0.07 0.08 -0.06 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.086 r_dihedral_angle_2_deg 9.581 r_dihedral_angle_1_deg 6.708 r_long_range_B_refined 6.193 r_long_range_B_other 5.988 r_scangle_other 4.716 r_scbond_it 3.055 r_scbond_other 3.055 r_mcangle_it 2.691 r_mcangle_other 2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.086 r_dihedral_angle_2_deg 9.581 r_dihedral_angle_1_deg 6.708 r_long_range_B_refined 6.193 r_long_range_B_other 5.988 r_scangle_other 4.716 r_scbond_it 3.055 r_scbond_other 3.055 r_mcangle_it 2.691 r_mcangle_other 2.69 r_angle_refined_deg 1.828 r_mcbond_it 1.801 r_mcbond_other 1.8 r_angle_other_deg 0.66 r_chiral_restr 0.102 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.003 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 5322 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 44
Software Software Software Name Purpose autoPROC data processing MOLREP phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction