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Crystal Structure of cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with alpha Cyclophellitol Cyclosulfate probe ME647
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 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 2% PEG400
Crystal Properties Matthews coefficient Solvent content 3.06 59.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.38 α = 90 b = 197.38 β = 90 c = 102.909 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 2016-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 49.85 100 0.077 0.016 1 30.2 24.1 92616
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.755 0.156 0.959 5.5 24.1
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 1.9 49.85 88031 4584 99.94 0.19769 0.19609 0.2055 0.22785 0.2337 RANDOM 31.902
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] -1.4 -0.7 -1.4 4.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.231 r_dihedral_angle_4_deg 15.722 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_1_deg 6.874 r_long_range_B_refined 6.21 r_long_range_B_other 6.209 r_scangle_other 4.526 r_mcangle_it 3.195 r_mcangle_other 3.195 r_scbond_it 2.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.231 r_dihedral_angle_4_deg 15.722 r_dihedral_angle_3_deg 14.122 r_dihedral_angle_1_deg 6.874 r_long_range_B_refined 6.21 r_long_range_B_other 6.209 r_scangle_other 4.526 r_mcangle_it 3.195 r_mcangle_other 3.195 r_scbond_it 2.896 r_scbond_other 2.893 r_mcbond_it 2.267 r_mcbond_other 2.263 r_angle_refined_deg 1.673 r_angle_other_deg 1.003 r_chiral_restr 0.1 r_bond_refined_d 0.014 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 6236 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing