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Structure of a complex of C-terminal lobe of bovine lactoferrin with disaccharide at 1.97 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 6.8 298 HEPES, PEG 550 monomethyl ether, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.609 α = 90 b = 50.017 β = 107.11 c = 65.395 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 200 IMAGE PLATE MAR scanner 345 mm plate 2006-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 1.97 25 90.9 24680 22864
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 1.97 2 99.2
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 PDB ENTRY 2B6D 1.97 62.02 24680 22864 1229 88.81 0.2217 0.21501 0.21409 0.23054 RANDOM 44.865
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] 2.91 -2.18 -2.72 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.106 r_dihedral_angle_1_deg 4.095 r_scangle_it 3.543 r_scbond_it 2.12 r_angle_refined_deg 1.7 r_mcangle_it 1.63 r_mcbond_it 0.871 r_symmetry_hbond_refined 0.579 r_metal_ion_refined 0.258 r_symmetry_vdw_refined 0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.106 r_dihedral_angle_1_deg 4.095 r_scangle_it 3.543 r_scbond_it 2.12 r_angle_refined_deg 1.7 r_mcangle_it 1.63 r_mcbond_it 0.871 r_symmetry_hbond_refined 0.579 r_metal_ion_refined 0.258 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 2605 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement MAR345 data collection HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing