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Crystal structure of the complex formed between C-lobe of bovine lactoferrin and 5-chloro-6'-methyl-3-[4-(methylsulfonyl)phenyl]-2,3'-bipyridine at 2.25 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.01M ZnSO4, 0.1M MES, 25% PEG, Monomethyl Ether 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.66 53.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.514 α = 90 b = 50.395 β = 107.97 c = 65.863 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 300 IMAGE PLATE MARRESEARCH MIRROR 2007-11-20 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) 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 2.25 20 94.6 0.106 7.9 19072 17086 31.3
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 2.25 2.29 91.9 0.328 1.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DYX 2.25 20 19072 17086 929 94.69 0.1875 0.1854 0.18321 0.1832 0.22458 0.2258 RANDOM 31.338
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] 0.7 -0.89 -0.49 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.027 r_dihedral_angle_4_deg 20.209 r_dihedral_angle_3_deg 17.481 r_dihedral_angle_1_deg 6.371 r_scangle_it 3.489 r_scbond_it 2.04 r_mcangle_it 1.468 r_angle_refined_deg 1.407 r_mcbond_it 0.82 r_angle_other_deg 0.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.027 r_dihedral_angle_4_deg 20.209 r_dihedral_angle_3_deg 17.481 r_dihedral_angle_1_deg 6.371 r_scangle_it 3.489 r_scbond_it 2.04 r_mcangle_it 1.468 r_angle_refined_deg 1.407 r_mcbond_it 0.82 r_angle_other_deg 0.366 r_symmetry_hbond_refined 0.323 r_symmetry_vdw_refined 0.303 r_nbtor_refined 0.302 r_nbd_refined 0.207 r_metal_ion_refined 0.189 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.09 r_nbd_other 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2604 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement DENZO data reduction AUTOMAR data reduction SCALEPACK data scaling MOLREP phasing