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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 C-lobe complex with diclofenac
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 0.1M MES, 25% POLY ETHYLENE GLYCOL MONOMETHYL ETHER-550, 0.1M ZNSO4, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.432 α = 90 b = 49.865 β = 107.1 c = 65.165 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 203 IMAGE PLATE MAR scanner 345 mm plate 2005-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8 EMBL/DESY, HAMBURG X13
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 1.4 62.26 99.6 74524 70446
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 1.4 1.43 100
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 1.4 62.26 74524 70446 3738 99.6 0.204 0.193 0.2021 0.219 0.2175 RANDOM 23.61
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 -0.53 -0.63 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.734 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_3_deg 13.736 r_dihedral_angle_1_deg 5.216 r_scangle_it 2.829 r_scbond_it 1.681 r_angle_refined_deg 1.467 r_mcangle_it 1.223 r_mcbond_it 0.635 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.734 r_dihedral_angle_4_deg 16.983 r_dihedral_angle_3_deg 13.736 r_dihedral_angle_1_deg 5.216 r_scangle_it 2.829 r_scbond_it 1.681 r_angle_refined_deg 1.467 r_mcangle_it 1.223 r_mcbond_it 0.635 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 509 Heterogen Atoms 200
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling