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Ligand recognition site in C-lobe of lactoferrin: Crystal structure of the complex of C-lobe of bovine lactoferrin with methyl alpha-D-mannopyranoside at 1.9 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, PEG monomethyl ether 550, 0.1M ZnSO4, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.411 α = 90 b = 50.439 β = 107.76 c = 65.956 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 2006-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.9 20 96.1 30002 29968
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 1.9 1.93 92.3
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 1.9 20 30002 29019 949 94.96 0.19 0.18938 0.18802 0.22944 RANDOM 36.018
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] 0.65 -0.87 -0.43 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.524 r_dihedral_angle_1_deg 3.785 r_scangle_it 3.449 r_scbond_it 2.057 r_mcangle_it 1.55 r_angle_refined_deg 1.4 r_mcbond_it 0.816 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.213 r_metal_ion_refined 0.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.524 r_dihedral_angle_1_deg 3.785 r_scangle_it 3.449 r_scbond_it 2.057 r_mcangle_it 1.55 r_angle_refined_deg 1.4 r_mcbond_it 0.816 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.213 r_metal_ion_refined 0.193 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 354 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement DENZO data reduction AUTOMAR data reduction AMoRE phasing