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Aspergillus kawachii beta-fructofuranosidase complexed with glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1 M sodium acetate, 2.6 M sodium formate
Crystal Properties Matthews coefficient Solvent content 3.95 68.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.799 α = 90 b = 108.799 β = 90 c = 152.043 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 210 2016-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 47.11 99.9 0.076 53.6 11.1 61305
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 2.1 2.14 100 0.48 7.9 11.1
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 3LDK 2.1 47.11 58211 2928 99.87 0.17253 0.17104 0.1835 0.20245 0.214 RANDOM 32.952
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.764 r_dihedral_angle_4_deg 18.392 r_dihedral_angle_3_deg 12.13 r_dihedral_angle_1_deg 7.207 r_long_range_B_refined 4.772 r_long_range_B_other 4.657 r_angle_other_deg 3.838 r_scangle_other 3.265 r_mcangle_other 2.928 r_mcangle_it 2.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.764 r_dihedral_angle_4_deg 18.392 r_dihedral_angle_3_deg 12.13 r_dihedral_angle_1_deg 7.207 r_long_range_B_refined 4.772 r_long_range_B_other 4.657 r_angle_other_deg 3.838 r_scangle_other 3.265 r_mcangle_other 2.928 r_mcangle_it 2.927 r_scbond_it 2.137 r_scbond_other 2.137 r_mcbond_it 1.927 r_mcbond_other 1.912 r_angle_refined_deg 1.426 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 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 4664 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing