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Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophoropentaose
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 5.3 298 0.15M MES-NaOH, pH 5.3, 42% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.218 α = 90 b = 125.988 β = 100.45 c = 91.04 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 1.9 50 97.5 0.099 0.059 16.2 3.8 61562
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 1.9 1.93 95.6 0.545 0.323 0.824 2.1 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5YSE 1.9 44.76 58354 3100 97.5 0.16823 0.16631 0.20315 0.1959 RANDOM 32.853
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] -0.03 -0.03 0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.844 r_dihedral_angle_4_deg 17.798 r_dihedral_angle_3_deg 14.741 r_dihedral_angle_1_deg 6.13 r_long_range_B_refined 5.069 r_long_range_B_other 4.996 r_angle_refined_deg 1.864 r_scangle_other 1.649 r_scbond_it 1.066 r_scbond_other 1.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.844 r_dihedral_angle_4_deg 17.798 r_dihedral_angle_3_deg 14.741 r_dihedral_angle_1_deg 6.13 r_long_range_B_refined 5.069 r_long_range_B_other 4.996 r_angle_refined_deg 1.864 r_scangle_other 1.649 r_scbond_it 1.066 r_scbond_other 1.066 r_angle_other_deg 1.065 r_mcangle_it 1.029 r_mcangle_other 1.029 r_mcbond_it 0.646 r_mcbond_other 0.646 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 6145 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Coot refinement HKL-2000 data processing