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Structure of the complex of C-terminal lobe of bovine lactoferrin with N-(4-hydroxyphenyl) acetamide at 2.38 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 6.5 298 HEPES, PEG Monomethyl Ether 550, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.65 53.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.216 α = 90 b = 50.398 β = 107.6 c = 65.838 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 MAR scanner 345 mm plate mirror 2006-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54132
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 2.38 63.25 97.8 15696 14913
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 2.38 2.46 94.3
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 2B6D 2.38 63.25 15696 14913 781 97.7 0.2 0.17382 0.15741 0.22257 RANDOM 37.159
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] 0.38 -1.38 -0.64 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.086 r_dihedral_angle_1_deg 4.967 r_scangle_it 4.539 r_scbond_it 2.619 r_mcangle_it 1.823 r_angle_refined_deg 1.619 r_mcbond_it 0.948 r_symmetry_hbond_refined 0.302 r_metal_ion_refined 0.292 r_nbd_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.086 r_dihedral_angle_1_deg 4.967 r_scangle_it 4.539 r_scbond_it 2.619 r_mcangle_it 1.823 r_angle_refined_deg 1.619 r_mcbond_it 0.948 r_symmetry_hbond_refined 0.302 r_metal_ion_refined 0.292 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.212 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.104 r_bond_refined_d 0.013 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 269 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing