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Structure of Banana lectin - Glc-alpha(1,2)-Glc complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X1V PDB ENTRY 1x1v
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 ZINC ACETATE DIHYDRATE, SODIUM CACODYLATE, 1,6-HEXANEDIOL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 5.01 75.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.569 α = 90 b = 82.569 β = 90 c = 149.446 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MARRESEARCH MIRRORS 2004-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 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 3.5 10 90.1 0.168 8.9 4.5 7895 6751
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 3.5 3.62 91.4 0.518 2.8 672
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 PDB ENTRY 1x1v 3.5 9.99 6056 669 100 0.22193 0.21738 0.2004 0.2623 0.2469 RANDOM 32.603
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] 3.45 1.72 3.45 -5.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.433 r_dihedral_angle_3_deg 20.737 r_dihedral_angle_4_deg 19.624 r_dihedral_angle_1_deg 6.765 r_scangle_it 1.36 r_angle_refined_deg 1.187 r_mcangle_it 0.837 r_scbond_it 0.798 r_mcbond_it 0.464 r_nbtor_refined 0.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.433 r_dihedral_angle_3_deg 20.737 r_dihedral_angle_4_deg 19.624 r_dihedral_angle_1_deg 6.765 r_scangle_it 1.36 r_angle_refined_deg 1.187 r_mcangle_it 0.837 r_scbond_it 0.798 r_mcbond_it 0.464 r_nbtor_refined 0.321 r_symmetry_metal_ion_refined 0.275 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.077 r_symmetry_hbond_refined 0.044 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2032 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling