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Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotetraose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 298 0.1M MES-NaOH, pH 5.3, 42% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.014 α = 89.99 b = 63.28 β = 82.24 c = 87.451 γ = 86.08
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 270 2015-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 50 96 0.068 0.043 20.7 3.4 98051
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 87 0.737 0.474 0.617 1.5 3.3
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 5YSB 1.6 43.32 92359 4783 96.38 0.15902 0.1575 0.2039 0.18763 0.2267 RANDOM 46.917
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 38.468 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_3_deg 14.559 r_dihedral_angle_1_deg 5.959 r_long_range_B_refined 5.385 r_long_range_B_other 5.385 r_angle_other_deg 3.626 r_scangle_other 2.451 r_angle_refined_deg 1.855 r_scbond_it 1.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.468 r_dihedral_angle_4_deg 16.856 r_dihedral_angle_3_deg 14.559 r_dihedral_angle_1_deg 5.959 r_long_range_B_refined 5.385 r_long_range_B_other 5.385 r_angle_other_deg 3.626 r_scangle_other 2.451 r_angle_refined_deg 1.855 r_scbond_it 1.631 r_scbond_other 1.631 r_mcangle_it 1.502 r_mcangle_other 1.502 r_mcbond_it 1.007 r_mcbond_other 1.007 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_other 0.016 r_gen_planes_refined 0.011 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 6124 Nucleic Acid Atoms Solvent Atoms 632 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing MOLREP phasing ARP/wARP model building