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Crystal structure of the complex of bovine lactoferrin C-lobe with a pentasaccharide at 2.38 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B6D PDB ENTRY 2B6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.1M MES, PEG MONOMETHYLETHER, 0.1M ZNSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.96 α = 90 b = 50.499 β = 107.5 c = 65.859 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 293 IMAGE PLATE MARRESEARCH Mirror 2005-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.38 63.24 86.8 16044 16044
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.42 96.6
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 PDB ENTRY 2B6D 2.38 62.02 16044 14993 484 96.47 0.213 0.19948 0.19831 0.23581 RANDOM 33.509
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] 0.89 -1.11 -0.56 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.743 r_dihedral_angle_1_deg 5.419 r_scangle_it 3.675 r_scbond_it 2.074 r_angle_refined_deg 1.898 r_mcangle_it 1.451 r_mcbond_it 0.749 r_symmetry_hbond_refined 0.381 r_symmetry_vdw_refined 0.292 r_nbd_refined 0.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.743 r_dihedral_angle_1_deg 5.419 r_scangle_it 3.675 r_scbond_it 2.074 r_angle_refined_deg 1.898 r_mcangle_it 1.451 r_mcbond_it 0.749 r_symmetry_hbond_refined 0.381 r_symmetry_vdw_refined 0.292 r_nbd_refined 0.283 r_xyhbond_nbd_refined 0.205 r_metal_ion_refined 0.175 r_chiral_restr 0.142 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing