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Faecalibacterium duncaniae branching enzyme FdBE2 maltohexaose complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 21JH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG4000, PEG3350, ammonium sulfate, Tris-HCl pH8.5
Crystal Properties Matthews coefficient Solvent content 2.36 47.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.395 α = 90 b = 73.476 β = 91.84 c = 56.971 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS 2M-F 2023-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 47.6 98.8 0.023 0.015 19.7 3.3 88773
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 1.63 86.5 0.265 0.192 2.8 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 47.61 84413 4359 98.73 0.14942 0.14848 0.1612 0.16749 0.1784 RANDOM 21.293
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 29.366 r_dihedral_angle_4_deg 18.806 r_dihedral_angle_3_deg 12.564 r_dihedral_angle_1_deg 6.883 r_long_range_B_refined 4.577 r_long_range_B_other 4.448 r_angle_other_deg 3.026 r_scangle_other 2.606 r_mcangle_it 2.186 r_mcangle_other 2.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.366 r_dihedral_angle_4_deg 18.806 r_dihedral_angle_3_deg 12.564 r_dihedral_angle_1_deg 6.883 r_long_range_B_refined 4.577 r_long_range_B_other 4.448 r_angle_other_deg 3.026 r_scangle_other 2.606 r_mcangle_it 2.186 r_mcangle_other 2.186 r_scbond_it 1.623 r_scbond_other 1.623 r_angle_refined_deg 1.297 r_mcbond_it 1.271 r_mcbond_other 1.271 r_chiral_restr 0.064 r_bond_other_d 0.035 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 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 4939 Nucleic Acid Atoms Solvent Atoms 533 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing