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Frischella perrara beta-fructofuranosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PIG
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 2.65 53.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.402 α = 90 b = 66.402 β = 90 c = 465.263 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 1.6 48.9 100 0.08 0.02 19.9 17.6 82441
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 1.6 1.69 100 0.587 0.143 4.5
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 3PIG 1.6 48.92 78311 3951 99.99 0.20123 0.20002 0.2128 0.22559 0.2362 RANDOM 26.224
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 38.656 r_dihedral_angle_4_deg 13.905 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_1_deg 8.233 r_long_range_B_refined 4.863 r_long_range_B_other 4.858 r_scangle_other 3.911 r_scbond_it 2.636 r_scbond_other 2.636 r_mcangle_it 2.632
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.656 r_dihedral_angle_4_deg 13.905 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_1_deg 8.233 r_long_range_B_refined 4.863 r_long_range_B_other 4.858 r_scangle_other 3.911 r_scbond_it 2.636 r_scbond_other 2.636 r_mcangle_it 2.632 r_mcangle_other 2.629 r_mcbond_it 1.878 r_mcbond_other 1.875 r_angle_refined_deg 1.559 r_angle_other_deg 1.36 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 261 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing