☰ Navigation Tabs
Structural basis of the prevention of NSAID-induced damage of the gastrointestinal tract by C-terminal half (C-lobe) of bovine colostrum protein lactoferrin: Binding and structural studies of the C-lobe complex with aspirin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NKX PDB ENTRY 1NKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 25% PEG MONOMETHYL ETHER-550, 0.1M ZNSO4, 0.1M MES, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.308 α = 90 b = 50.469 β = 107.7 c = 65.942 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 291 IMAGE PLATE MAR scanner 345 mm plate MIRROR 2006-02-08 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) 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 63.25 96.1 27067 24688
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 2.06 95.2
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 (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 1NKX 2 63.25 27067 24688 1303 96 0.184 0.182 0.1868 0.228 0.2338 RANDOM 33.65
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] 1.05 -1.53 -0.8 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.909 r_dihedral_angle_1_deg 5.387 r_scangle_it 4.276 r_scbond_it 2.441 r_angle_refined_deg 1.739 r_mcangle_it 1.681 r_mcbond_it 0.888 r_symmetry_hbond_refined 0.393 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.909 r_dihedral_angle_1_deg 5.387 r_scangle_it 4.276 r_scbond_it 2.441 r_angle_refined_deg 1.739 r_mcangle_it 1.681 r_mcbond_it 0.888 r_symmetry_hbond_refined 0.393 r_nbd_refined 0.241 r_symmetry_vdw_refined 0.23 r_metal_ion_refined 0.225 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.163 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 2604 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 189
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling