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Frischella perrara beta-fructofuranosidase in complex with fructose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VCO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2-propanol, PEG 600, PEG 3350, ammonium acetate, HEPES-NaOH
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.255 α = 90 b = 66.255 β = 90 c = 463.867 γ = 120
Symmetry Space Group P 61 2 2
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 S 6M 2019-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2 48.8 100 0.094 0.022 21.8 18.4 42744
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 2 2.11 0.714 0.166 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 (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 7VCO 2 48.8 40529 2091 99.98 0.18083 0.17923 0.1881 0.21228 0.2162 RANDOM 34.088
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 36.861 r_dihedral_angle_4_deg 14.208 r_dihedral_angle_3_deg 13.44 r_dihedral_angle_1_deg 8.277 r_long_range_B_refined 5.734 r_long_range_B_other 5.721 r_scangle_other 4.594 r_mcangle_it 3.052 r_mcangle_other 3.052 r_scbond_it 3.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.861 r_dihedral_angle_4_deg 14.208 r_dihedral_angle_3_deg 13.44 r_dihedral_angle_1_deg 8.277 r_long_range_B_refined 5.734 r_long_range_B_other 5.721 r_scangle_other 4.594 r_mcangle_it 3.052 r_mcangle_other 3.052 r_scbond_it 3.034 r_scbond_other 3.033 r_mcbond_other 2.243 r_mcbond_it 2.242 r_angle_refined_deg 1.454 r_angle_other_deg 1.273 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 3941 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing