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Crystal structure of single chain recombinant jacalin showing highly dynamic posttranslational excission loop that reduces binding affinity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JAC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 0.2M Ammonium acetate, 0.1M Sodium acetate buffer, 15%(w/v) PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.29 46.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.878 α = 90 b = 42.157 β = 122.39 c = 73.586 γ = 90
Symmetry Space Group C 1 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 295 IMAGE PLATE RIGAKU RAXIS IV++ Mirrors 2007-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 62.6 94.1 0.072 11.6 1.13 19935 19
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) 2 2.03 94.1 0.072 11.6 1.13 19935
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1JAC 2 56.57 19935 18885 1022 93.97 0.18013 0.17843 0.1804 0.2115 0.2147 RANDOM 24.286
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] 0.02 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.79 r_dihedral_angle_3_deg 16.616 r_dihedral_angle_4_deg 10.004 r_dihedral_angle_1_deg 6.495 r_scangle_it 2.632 r_scbond_it 1.6 r_angle_refined_deg 1.184 r_mcangle_it 1.135 r_mcbond_it 0.588 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.79 r_dihedral_angle_3_deg 16.616 r_dihedral_angle_4_deg 10.004 r_dihedral_angle_1_deg 6.495 r_scangle_it 2.632 r_scbond_it 1.6 r_angle_refined_deg 1.184 r_mcangle_it 1.135 r_mcbond_it 0.588 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2318 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling