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Crystal structure of a designed Cyanovirin-N homolog lectin; LKAMG, bound to sucrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HNU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 277 protein solutions (~40 mg/ml) were incubated overnight with sucrose at a molar ratio of 1:40 (protein:disaccharide) and crystallization were carried out using 0.2 M Li2SO4, 0.1 M Tris-HCl (pH 8.5), and 30% PEG 4000 with protein to mother liquor ratio of 8 to 1 , VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.01 59.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.497 α = 90 b = 39.298 β = 97.64 c = 86.134 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU RAXIS IV 2007-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT
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 1.88 35.7 96.7 0.166 3.9 3.08 23572 3
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) 1.88 1.95 76.1 0.413 1.4 2.92
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 3HNU 2 35.7 19030 1022 98.8 0.227 0.224 0.2258 0.277 0.2796 RANDOM 30.47
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] 0.03 -2.26 -1.64 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_4_deg 20.972 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 6.766 r_scangle_it 4.858 r_scbond_it 3.257 r_mcangle_it 1.873 r_angle_refined_deg 1.596 r_mcbond_it 1.15 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.09 r_dihedral_angle_4_deg 20.972 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 6.766 r_scangle_it 4.858 r_scbond_it 3.257 r_mcangle_it 1.873 r_angle_refined_deg 1.596 r_mcbond_it 1.15 r_chiral_restr 0.115 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 1717 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 108
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling