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Carbohydrate recognition of C-terminal half of lactoferrin: Crystal structure of the complex of C-lobe with rhamnose at 2.15 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 0.1M MES, 25% POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, 0.01M ZINC SULPHATE, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.511 α = 90 b = 50.352 β = 107.88 c = 65.896 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 298 IMAGE PLATE MARRESEARCH mirror 2006-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5414
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.15 20 98.8 0.15 6.4 21564 21564 26.197
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 90.8 0.323 2.1
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1NKX 2.15 20 21520 20824 696 98.72 0.18142 0.18091 0.17972 0.20338 RANDOM 27.092
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] 1.08 -0.66 -0.65 -0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.958 r_dihedral_angle_4_deg 20.267 r_dihedral_angle_3_deg 17.308 r_scangle_it 6.823 r_dihedral_angle_1_deg 6.543 r_scbond_it 4.723 r_mcangle_it 3.342 r_mcbond_it 2.269 r_angle_refined_deg 1.674 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.958 r_dihedral_angle_4_deg 20.267 r_dihedral_angle_3_deg 17.308 r_scangle_it 6.823 r_dihedral_angle_1_deg 6.543 r_scbond_it 4.723 r_mcangle_it 3.342 r_mcbond_it 2.269 r_angle_refined_deg 1.674 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.31 r_metal_ion_refined 0.289 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.202 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.111 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 2605 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling AMoRE phasing