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4,6-alpha-glucanotransferase GTFB from Lactobacillus reuteri 121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KLK PDB ID 3KLK domains A, B, C, IV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 PEG3350, NaCl, (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.18 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 219.244 α = 90 b = 57.852 β = 114.75 c = 150.701 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS3 2M 2014-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8729 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 45.83 99.4 0.08 0.997 10.2 4.3 158306
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 1.8 1.83 97.1 0.808 1.6 4.3
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 PDB ID 3KLK domains A, B, C, IV 1.8 45.83 150356 7949 99.25 0.17883 0.17732 0.187 0.2076 0.2157 RANDOM 30.833
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] 0.86 1.04 -1.85 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.719 r_dihedral_angle_4_deg 15.556 r_dihedral_angle_3_deg 12.11 r_dihedral_angle_1_deg 5.95 r_long_range_B_refined 5.209 r_long_range_B_other 5.098 r_scangle_other 2.968 r_scbond_it 1.903 r_scbond_other 1.902 r_mcangle_other 1.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.719 r_dihedral_angle_4_deg 15.556 r_dihedral_angle_3_deg 12.11 r_dihedral_angle_1_deg 5.95 r_long_range_B_refined 5.209 r_long_range_B_other 5.098 r_scangle_other 2.968 r_scbond_it 1.903 r_scbond_other 1.902 r_mcangle_other 1.836 r_mcangle_it 1.835 r_angle_refined_deg 1.263 r_mcbond_it 1.249 r_mcbond_other 1.235 r_angle_other_deg 1.06 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 13364 Nucleic Acid Atoms Solvent Atoms 1283 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing