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Branching Sucrase Brs-B in complex with isomaltopentaose in the active site (alternative conformation)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 0.1M SPG Buffer pH 7, 20% PEG 1500
Crystal Properties Matthews coefficient Solvent content 4.03 69.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 253.639 α = 90 b = 253.639 β = 90 c = 344.433 γ = 120
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 6M 2018-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 3.3 50 100 0.189 3.7 8.6 63973
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.48 0.82 1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.3 48.412 63971 3137 99.947 0.202 0.2007 0.2034 0.2252 0.2257 66.677
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] 0.755 0.378 0.755 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.951 r_dihedral_angle_6_deg 12.41 r_dihedral_angle_1_deg 6.622 r_lrange_it 5.554 r_lrange_other 5.554 r_dihedral_angle_2_deg 4.144 r_mcangle_it 2.481 r_mcangle_other 2.481 r_scangle_it 2.123 r_scangle_other 2.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.951 r_dihedral_angle_6_deg 12.41 r_dihedral_angle_1_deg 6.622 r_lrange_it 5.554 r_lrange_other 5.554 r_dihedral_angle_2_deg 4.144 r_mcangle_it 2.481 r_mcangle_other 2.481 r_scangle_it 2.123 r_scangle_other 2.123 r_mcbond_it 1.378 r_mcbond_other 1.378 r_scbond_it 1.145 r_scbond_other 1.145 r_angle_refined_deg 0.9 r_angle_other_deg 0.393 r_symmetry_nbd_other 0.221 r_nbd_refined 0.206 r_nbd_other 0.18 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.137 r_symmetry_xyhbond_nbd_other 0.133 r_symmetry_nbd_refined 0.132 r_ncsr_local_group_1 0.104 r_symmetry_nbtor_other 0.075 r_symmetry_xyhbond_nbd_refined 0.074 r_chiral_restr 0.045 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18147 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 484
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing