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Structure of the complex of C-terminal lobe of bovine lactoferrin with mannose at 2.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B6D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 PEG 3350 monomethyl ether, ZnSO4, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.818 α = 90 b = 50.387 β = 108.08 c = 65.982 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 292 IMAGE PLATE MAR scanner 345 mm plate 2006-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.541
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 2.8 25 94.9 9679 9679
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 2.8 2.85 94.9
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 2B6D 2.8 25 9679 9121 549 94.43 0.21 0.19781 0.19582 0.22826 RANDOM 31.247
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] 1.75 -0.09 -1.09 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.794 r_dihedral_angle_1_deg 3.907 r_scangle_it 3.201 r_angle_refined_deg 1.791 r_scbond_it 1.739 r_mcangle_it 1.285 r_mcbond_it 0.67 r_symmetry_vdw_refined 0.346 r_symmetry_hbond_refined 0.341 r_nbd_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 21.794 r_dihedral_angle_1_deg 3.907 r_scangle_it 3.201 r_angle_refined_deg 1.791 r_scbond_it 1.739 r_mcangle_it 1.285 r_mcbond_it 0.67 r_symmetry_vdw_refined 0.346 r_symmetry_hbond_refined 0.341 r_nbd_refined 0.297 r_xyhbond_nbd_refined 0.214 r_metal_ion_refined 0.191 r_chiral_restr 0.105 r_bond_refined_d 0.011 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 2605 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing