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Beijerinckia indica beta-fructosyltransferase variant H395R/F473Y in complex with fructose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 30% (w/v) polyethylene glycol 10000, 0.2 M magnesium chloride, 0.1 M potassium sodium tartrate, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 1.95 36.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.542 α = 90 b = 81.697 β = 90 c = 99.602 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.36 47.8 99.7 0.053 0.023 15.6 6.4 95951
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.43 100 0.48 0.201 3.5 6.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.36 37.82 90892 4669 99.35 0.1627 0.16174 0.1649 0.18156 0.1849 RANDOM 17.745
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.081 r_dihedral_angle_4_deg 14.425 r_dihedral_angle_3_deg 11.613 r_dihedral_angle_1_deg 7.288 r_long_range_B_refined 4.281 r_long_range_B_other 4.038 r_scangle_other 2.594 r_angle_other_deg 2.302 r_mcangle_other 1.935 r_mcangle_it 1.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.081 r_dihedral_angle_4_deg 14.425 r_dihedral_angle_3_deg 11.613 r_dihedral_angle_1_deg 7.288 r_long_range_B_refined 4.281 r_long_range_B_other 4.038 r_scangle_other 2.594 r_angle_other_deg 2.302 r_mcangle_other 1.935 r_mcangle_it 1.932 r_scbond_it 1.666 r_scbond_other 1.665 r_angle_refined_deg 1.521 r_mcbond_it 1.221 r_mcbond_other 1.215 r_chiral_restr 0.072 r_bond_other_d 0.035 r_gen_planes_other 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 3703 Nucleic Acid Atoms Solvent Atoms 570 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing