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Crystal Structure of D412N nucleophile mutant cjAgd31B (alpha-transglucosylase from Glycoside Hydrolase Family 31) in complex with unreacted 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 293 1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 2% PEG400
Crystal Properties Matthews coefficient Solvent content 3.05 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.14 α = 90 b = 197.14 β = 90 c = 102.78 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 2016-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 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 1.96 65.67 99.9 0.2 0.046 0.999 11.4 20 84174
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 1.96 2.01 99.9 2.991 0.698 0.625 1.2 19.2
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 1.96 65.67 79999 4175 99.92 0.19081 0.18894 0.1978 0.22676 0.2307 RANDOM 38.436
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] -1.66 -0.83 -1.66 5.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.829 r_dihedral_angle_4_deg 16.613 r_dihedral_angle_3_deg 13.957 r_dihedral_angle_1_deg 6.736 r_long_range_B_refined 6.56 r_long_range_B_other 6.56 r_scangle_other 5.023 r_mcangle_it 3.323 r_mcangle_other 3.322 r_scbond_it 3.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.829 r_dihedral_angle_4_deg 16.613 r_dihedral_angle_3_deg 13.957 r_dihedral_angle_1_deg 6.736 r_long_range_B_refined 6.56 r_long_range_B_other 6.56 r_scangle_other 5.023 r_mcangle_it 3.323 r_mcangle_other 3.322 r_scbond_it 3.159 r_scbond_other 3.157 r_mcbond_it 2.253 r_mcbond_other 2.252 r_angle_refined_deg 1.57 r_angle_other_deg 0.959 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 362 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing