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Crystal structure of the C-terminally truncated human E430Q/E574Q-PGGHG double mutant in complex with kojibiose
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 7.35 289 Ratio: 1:1
Conditions: 25% PEG 3350, 0.1 M Bis-Tris-propane pH 7.35 and 0.2 M NaCl
Soaking for 2 hours with 10 mM KJB
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.005 α = 90 b = 77.169 β = 99.249 c = 79.055 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 2022-02-05 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 1.7 78.03 99.8 0.062 0.9936 10.3 6.5 70287 21.2
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 1.7 1.73 100 0.444 0.55 1.8 6.9
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 1.7 54.928 70264 3439 99.752 0.194 0.1931 0.2015 0.2114 0.2166 RANDOM 21.583
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] -0.261 -0.04 -0.068 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.105 r_dihedral_angle_3_deg 12.596 r_dihedral_angle_1_deg 6.943 r_dihedral_angle_2_deg 5.823 r_lrange_it 4.985 r_lrange_other 4.985 r_scangle_it 2.817 r_scangle_other 2.817 r_mcangle_it 2.169 r_mcangle_other 2.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.105 r_dihedral_angle_3_deg 12.596 r_dihedral_angle_1_deg 6.943 r_dihedral_angle_2_deg 5.823 r_lrange_it 4.985 r_lrange_other 4.985 r_scangle_it 2.817 r_scangle_other 2.817 r_mcangle_it 2.169 r_mcangle_other 2.168 r_scbond_it 1.72 r_scbond_other 1.719 r_mcbond_it 1.35 r_mcbond_other 1.349 r_angle_refined_deg 1.348 r_angle_other_deg 0.479 r_nbd_refined 0.202 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.17 r_symmetry_nbd_refined 0.166 r_nbd_other 0.155 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.068 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5322 Nucleic Acid Atoms Solvent Atoms 559 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement autoPROC data processing MOLREP phasing Coot model building autoPROC data reduction Aimless data scaling