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4,6-alpha-glucanotransferase GtfB from Limosilactobacillus reuteri NCC 2613 complexed with acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model PHYRE Obtained from Phyre homology modeling
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.4-1.7 M (NH4)2SO4, 0.1 M Bis-Tris-HCl, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.71 54.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.219 α = 90 b = 133.806 β = 90 c = 147.866 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 PILATUS 6M-F 2017-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.9762 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.9 49.29 98.3 0.43 0.454 0.141 0.975 3.6 9.1 46821
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 98.9 1.648 1.744 0.551 0.639 9
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 Obtained from Phyre homology modeling 2.9 49.29 44476 2250 97.75 0.2943 0.2932 0.2947 0.3146 0.3139 RANDOM 41.72
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] -2.98 5.63 -2.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.009 r_dihedral_angle_3_deg 14.568 r_dihedral_angle_4_deg 12.282 r_dihedral_angle_1_deg 6.098 r_angle_refined_deg 1.143 r_angle_other_deg 0.917 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.009 r_dihedral_angle_3_deg 14.568 r_dihedral_angle_4_deg 12.282 r_dihedral_angle_1_deg 6.098 r_angle_refined_deg 1.143 r_angle_other_deg 0.917 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13022 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 95
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction