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Structure of the cyanobacterial Oscillatoria Agardhii Agglutinin (OAA) in complex with a3,a6 mannopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S5V PDB ENTRY 3S5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 2.0 M (NH4)SO4 and 0.1 M Tris-HCl (pH 8.5) with protein and 3,6-mannopentaose at molar ratios of 1:2, 1:3, or 1:4 (the protein concentration kept at 40 mg/ml), VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.13 42.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.192 α = 90 b = 49.07 β = 90 c = 69.247 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV 2010-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
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 1.65 35.19 96.4 0.056 27.5 12.02 13024 13024 3 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 87.4 0.118 13.2 8.91
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 3S5V 1.65 35.19 1 13024 13024 1460 96.51 0.18156 0.17765 0.1803 0.21874 0.2203 RANDOM 18.374
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] -0.6 1 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.016 r_dihedral_angle_3_deg 9.911 r_dihedral_angle_4_deg 8.753 r_dihedral_angle_1_deg 6.207 r_scangle_it 2.615 r_scbond_it 1.895 r_angle_refined_deg 1.532 r_mcangle_it 1.345 r_mcbond_it 0.795 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.016 r_dihedral_angle_3_deg 9.911 r_dihedral_angle_4_deg 8.753 r_dihedral_angle_1_deg 6.207 r_scangle_it 2.615 r_scbond_it 1.895 r_angle_refined_deg 1.532 r_mcangle_it 1.345 r_mcbond_it 0.795 r_chiral_restr 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 983 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 112
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling