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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 indomethacin
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 MES, 0.01M ZNSO4, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.71 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.839 α = 90 b = 50.654 β = 107.56 c = 66.119 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 2005-08-01 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 2.2 62.99 91 20430 17853
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 2.3 93
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NKX 2.2 62.99 20430 17853 952 91 0.212 0.209 0.244 0.2144 RANDOM 39.4
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] 2.51 -0.53 -1.26 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.429 r_dihedral_angle_1_deg 5.708 r_scangle_it 4.414 r_scbond_it 2.626 r_angle_refined_deg 2.231 r_mcangle_it 1.927 r_mcbond_it 1.046 r_symmetry_vdw_refined 0.483 r_metal_ion_refined 0.291 r_nbd_refined 0.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.429 r_dihedral_angle_1_deg 5.708 r_scangle_it 4.414 r_scbond_it 2.626 r_angle_refined_deg 2.231 r_mcangle_it 1.927 r_mcbond_it 1.046 r_symmetry_vdw_refined 0.483 r_metal_ion_refined 0.291 r_nbd_refined 0.258 r_symmetry_hbond_refined 0.206 r_chiral_restr 0.202 r_xyhbond_nbd_refined 0.19 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 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 244 Heterogen Atoms 162
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling