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Beijerinckia indica beta-fructosyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 30% (w/v) polyethylene glycol 10000, 0.2 M MgCl2, 0.1 M Na K tartrate, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 1.74 29.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.891 α = 90 b = 80.9 β = 90 c = 92.661 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 2019-03-19 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) 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 2.2 46.3 99.8 0.125 0.054 0.992 9.6 6.4 20772
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 2.2 2.23 99.7 0.338 0.14 0.935 4.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1W18 2.2 44.3 20660 1011 99.298 0.224 0.2217 0.2285 0.2657 0.266 28.338
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] -0.006 0.014 -0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.734 r_dihedral_angle_3_deg 15.42 r_dihedral_angle_4_deg 13.269 r_dihedral_angle_1_deg 8.058 r_lrange_it 5.293 r_lrange_other 5.288 r_scangle_it 3.815 r_scangle_other 3.814 r_mcangle_it 3.269 r_mcangle_other 3.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.734 r_dihedral_angle_3_deg 15.42 r_dihedral_angle_4_deg 13.269 r_dihedral_angle_1_deg 8.058 r_lrange_it 5.293 r_lrange_other 5.288 r_scangle_it 3.815 r_scangle_other 3.814 r_mcangle_it 3.269 r_mcangle_other 3.269 r_scbond_it 2.601 r_scbond_other 2.601 r_angle_other_deg 2.41 r_mcbond_it 2.233 r_mcbond_other 2.231 r_angle_refined_deg 1.636 r_symmetry_nbd_refined 0.286 r_nbd_other 0.271 r_symmetry_xyhbond_nbd_refined 0.242 r_symmetry_nbd_other 0.217 r_nbd_refined 0.202 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.16 r_metal_ion_refined 0.149 r_symmetry_xyhbond_nbd_other 0.077 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.069 r_bond_other_d 0.036 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3694 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing