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Structure of the complex of lactoferrin C-terminal half with fucose at 2.07 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 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.365 α = 90 b = 50.383 β = 107.72 c = 65.814 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 2006-07-25 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 2.07 20 94.8 0.07 11.8 23099 23077 29.055
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 2.07 2.14 93.9 0.256 2
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 2.07 20 23099 22333 743 94.89 0.17411 0.17549 0.17404 0.20931 RANDOM 34.491
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] 0.62 -1.04 -0.71 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.981 r_dihedral_angle_4_deg 24.172 r_dihedral_angle_3_deg 18.155 r_dihedral_angle_1_deg 6.367 r_scangle_it 5.531 r_scbond_it 3.286 r_mcangle_it 2.249 r_angle_refined_deg 1.412 r_mcbond_it 1.358 r_symmetry_hbond_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.981 r_dihedral_angle_4_deg 24.172 r_dihedral_angle_3_deg 18.155 r_dihedral_angle_1_deg 6.367 r_scangle_it 5.531 r_scbond_it 3.286 r_mcangle_it 2.249 r_angle_refined_deg 1.412 r_mcbond_it 1.358 r_symmetry_hbond_refined 0.323 r_metal_ion_refined 0.32 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.292 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.091 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 2604 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement AUTOMAR data reduction SCALEPACK data scaling AMoRE phasing