☰ Navigation Tabs
Crystal Structure of Agd31B, alpha-transglucosylase, complexed with a non-covalent 1,2- Cyclophellitol aziridine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.8 Ammonium sulfate, 0.1 M HEPES pH 7.0, 2% PEG 400
Crystal Properties Matthews coefficient Solvent content 3.11 60.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.02 α = 90 b = 341.249 β = 90 c = 102.805 γ = 90
Symmetry Space Group C 2 2 2
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 XE 16M 2022-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 49.83 100 0.99 9.1 14 270451
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 1.9 1.93 0.44
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 49.82 256553 13898 99.98 0.21932 0.21706 0.26108 0.2434 RANDOM 35.557
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] -1.64 -1.37 3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.36 r_dihedral_angle_2_deg 9.469 r_dihedral_angle_1_deg 7.577 r_long_range_B_refined 6.15 r_long_range_B_other 6.149 r_scangle_other 4.926 r_mcangle_it 3.896 r_mcangle_other 3.896 r_scbond_it 3.334 r_scbond_other 3.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.36 r_dihedral_angle_2_deg 9.469 r_dihedral_angle_1_deg 7.577 r_long_range_B_refined 6.15 r_long_range_B_other 6.149 r_scangle_other 4.926 r_mcangle_it 3.896 r_mcangle_other 3.896 r_scbond_it 3.334 r_scbond_other 3.329 r_mcbond_it 2.913 r_mcbond_other 2.912 r_angle_refined_deg 1.624 r_angle_other_deg 0.561 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 18545 Nucleic Acid Atoms Solvent Atoms 994 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing