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Structure of Banana Lectin-pentamannose 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, SITTING DROP 8 298 ZINC ACETATE DIHYDRATE, SODIUM CACODYLATE, 1,6-HEXANEDIOL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.74 74.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.911 α = 90 b = 80.911 β = 90 c = 147.405 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 100 IMAGE PLATE MARRESEARCH MIRRORS 2005-08-08 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 2.63 30 99.7 0.066 33 8.76 17203 17137
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 2.63 2.72 98.7 0.428 4.9 1646
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 2.63 24.92 15770 1320 100 0.21875 0.21667 0.2075 0.24335 0.2322 RANDOM 57.022
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] 3.74 1.87 3.74 -5.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.677 r_dihedral_angle_3_deg 17.966 r_dihedral_angle_4_deg 15.777 r_dihedral_angle_1_deg 6.12 r_scangle_it 1.72 r_angle_refined_deg 1.279 r_scbond_it 0.983 r_mcangle_it 0.68 r_mcbond_it 0.36 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.677 r_dihedral_angle_3_deg 17.966 r_dihedral_angle_4_deg 15.777 r_dihedral_angle_1_deg 6.12 r_scangle_it 1.72 r_angle_refined_deg 1.279 r_scbond_it 0.983 r_mcangle_it 0.68 r_mcbond_it 0.36 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.115 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_metal_ion_refined 0.004 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 2030 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 121
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling