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Aspergillus kawachii beta-fructofuranosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1 M sodium phosphate, 2.6 M sodium formate
Crystal Properties Matthews coefficient Solvent content 3.98 69.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.786 α = 90 b = 108.786 β = 90 c = 153.196 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 2016-06-25 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 2.3 50.01 99.9 0.093 24.5 9 47061
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 2.3 2.34 0.365 0.365 8.4
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 5XH8 2.3 50.01 44618 2354 99.75 0.19024 0.18871 0.1982 0.21877 0.2283 RANDOM 35.508
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.067 r_dihedral_angle_4_deg 16.926 r_dihedral_angle_3_deg 11.907 r_dihedral_angle_1_deg 6.987 r_long_range_B_refined 4.777 r_long_range_B_other 4.768 r_angle_other_deg 3.894 r_mcangle_other 3.461 r_mcangle_it 3.459 r_scangle_other 3.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.067 r_dihedral_angle_4_deg 16.926 r_dihedral_angle_3_deg 11.907 r_dihedral_angle_1_deg 6.987 r_long_range_B_refined 4.777 r_long_range_B_other 4.768 r_angle_other_deg 3.894 r_mcangle_other 3.461 r_mcangle_it 3.459 r_scangle_other 3.292 r_mcbond_it 2.207 r_mcbond_other 2.18 r_scbond_it 2.049 r_scbond_other 2.024 r_angle_refined_deg 1.396 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 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 4656 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing