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Crystal Structure of the complex of C-lobe of bovine lactoferrin with Mannitol and Mannose at 2.7 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DWH pdb entry 2DWH
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 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.4 α = 90 b = 50.3 β = 107.8 c = 65.9 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 2007-04-26 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) 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 2.7 20 94.4 0.147 4.8 6.36 9718
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 2.7 2.8 95.2 0.438 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2DWH 2.71 20 9718 467 94.4 0.19719 0.19491 0.1923 0.23983 0.2399 RANDOM 26.682
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] 1.48 0.25 -0.38 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.026 r_dihedral_angle_3_deg 20.337 r_dihedral_angle_4_deg 19.984 r_dihedral_angle_1_deg 6.069 r_scangle_it 4.805 r_scbond_it 2.939 r_mcangle_it 2.279 r_angle_refined_deg 2.276 r_mcbond_it 1.577 r_symmetry_vdw_refined 0.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.026 r_dihedral_angle_3_deg 20.337 r_dihedral_angle_4_deg 19.984 r_dihedral_angle_1_deg 6.069 r_scangle_it 4.805 r_scbond_it 2.939 r_mcangle_it 2.279 r_angle_refined_deg 2.276 r_mcbond_it 1.577 r_symmetry_vdw_refined 0.375 r_nbtor_refined 0.326 r_nbd_refined 0.271 r_metal_ion_refined 0.24 r_xyhbond_nbd_refined 0.216 r_symmetry_hbond_refined 0.203 r_chiral_restr 0.13 r_bond_refined_d 0.024 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement AUTOMAR data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing