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Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YSE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.15M MES-NaOH, pH 5.5, 50% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.34 47.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.082 α = 90 b = 125.561 β = 101.61 c = 91.78 γ = 90
Symmetry Space Group P 1 21 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 270 2015-12-19 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 2.1 50 96.5 0.116 0.071 12.4 3.6 44909
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 2.1 2.14 96.5 0.639 0.389 0.697 3.5
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 5YSE 2.1 44.95 42614 2264 96.43 0.17139 0.16942 0.2032 0.20732 0.2301 RANDOM 56.682
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 38.631 r_dihedral_angle_4_deg 18.968 r_dihedral_angle_3_deg 16.44 r_dihedral_angle_1_deg 6.046 r_long_range_B_other 4.103 r_long_range_B_refined 4.102 r_angle_other_deg 3.704 r_scangle_other 1.93 r_angle_refined_deg 1.851 r_mcangle_it 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.631 r_dihedral_angle_4_deg 18.968 r_dihedral_angle_3_deg 16.44 r_dihedral_angle_1_deg 6.046 r_long_range_B_other 4.103 r_long_range_B_refined 4.102 r_angle_other_deg 3.704 r_scangle_other 1.93 r_angle_refined_deg 1.851 r_mcangle_it 1.44 r_mcangle_other 1.44 r_scbond_it 1.197 r_scbond_other 1.197 r_mcbond_it 0.872 r_mcbond_other 0.871 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_other 0.013 r_gen_planes_refined 0.009 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 6135 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing MOLREP phasing Coot refinement