☰ Navigation Tabs
Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with Cyclophellitol Aziridine probe CF022
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 7 293 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 2% PEG400
Crystal Properties Matthews coefficient Solvent content 3.3 62.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198 α = 90 b = 198 β = 90 c = 103 γ = 120
Symmetry Space Group P 6 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 PILATUS 6M-F 2015-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 .9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 171.47 100 0.13 19.6 20 86417
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.99 100 1.64 0.801 20.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4B9Y 1.95 171.47 82110 4304 99.96 0.16375 0.16254 0.1725 0.18711 0.1941 RANDOM 35.753
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 -0.12 -0.24 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.832 r_dihedral_angle_4_deg 17.71 r_dihedral_angle_3_deg 13.34 r_dihedral_angle_1_deg 6.714 r_long_range_B_refined 6.161 r_long_range_B_other 6.16 r_scangle_other 2.506 r_angle_refined_deg 1.573 r_scbond_it 1.527 r_scbond_other 1.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.832 r_dihedral_angle_4_deg 17.71 r_dihedral_angle_3_deg 13.34 r_dihedral_angle_1_deg 6.714 r_long_range_B_refined 6.161 r_long_range_B_other 6.16 r_scangle_other 2.506 r_angle_refined_deg 1.573 r_scbond_it 1.527 r_scbond_other 1.527 r_mcangle_it 1.458 r_mcangle_other 1.458 r_angle_other_deg 0.967 r_mcbond_it 0.925 r_mcbond_other 0.92 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 6229 Nucleic Acid Atoms Solvent Atoms 631 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing