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Structure of Banana lectin-alpha-D-mannose 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 4.77 74.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.926 α = 90 b = 80.926 β = 90 c = 148.173 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 2005-07-25 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 2.32 30 98.4 0.077 16.4 4.7 25080 24663
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 2.32 2.4 98.4 0.489 3.3 2392
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 2.32 25.46 23385 1257 100 0.20541 0.2033 0.1967 0.24628 0.2326 RANDOM 48.204
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] 2.08 1.04 2.08 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.22 r_dihedral_angle_3_deg 15.238 r_dihedral_angle_4_deg 10.111 r_dihedral_angle_1_deg 6.253 r_scangle_it 1.51 r_angle_refined_deg 1.192 r_scbond_it 0.949 r_mcangle_it 0.675 r_mcbond_it 0.396 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.22 r_dihedral_angle_3_deg 15.238 r_dihedral_angle_4_deg 10.111 r_dihedral_angle_1_deg 6.253 r_scangle_it 1.51 r_angle_refined_deg 1.192 r_scbond_it 0.949 r_mcangle_it 0.675 r_mcbond_it 0.396 r_nbtor_refined 0.309 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.155 r_metal_ion_refined 0.15 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.087 r_chiral_restr 0.075 r_symmetry_metal_ion_refined 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2017 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 114
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling