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Crystal structure of Siderocalin (NGAL, Lipocalin 2) W79A-R81A complexed with Ferric Enterobactin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L6M PDB ENTRY 1L6M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 291 1.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.9 57.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.358 α = 90 b = 114.358 β = 90 c = 119.042 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2005-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.572 28.59 100 0.078 0.289 12.6 25655 23194 63.391
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.572 2.66 100 0.397 7.1 12.5 2519
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 Used previously-determined structure THROUGHOUT PDB ENTRY 1L6M 2.572 28.59 25655 23194 2410 99.72 0.24891 0.24751 0.2467 0.26249 0.2662 Used same set as previously-determined structure 46.342
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] 0.47 0.47 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_4_deg 17.843 r_dihedral_angle_3_deg 15.186 r_dihedral_angle_1_deg 4.795 r_scangle_it 0.991 r_angle_refined_deg 0.84 r_angle_other_deg 0.82 r_scbond_it 0.668 r_mcangle_it 0.582 r_mcbond_it 0.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.195 r_dihedral_angle_4_deg 17.843 r_dihedral_angle_3_deg 15.186 r_dihedral_angle_1_deg 4.795 r_scangle_it 0.991 r_angle_refined_deg 0.84 r_angle_other_deg 0.82 r_scbond_it 0.668 r_mcangle_it 0.582 r_mcbond_it 0.456 r_metal_ion_refined 0.213 r_nbd_other 0.207 r_symmetry_vdw_other 0.188 r_nbtor_refined 0.177 r_nbd_refined 0.176 r_xyhbond_nbd_refined 0.111 r_symmetry_vdw_refined 0.101 r_mcbond_other 0.09 r_nbtor_other 0.078 r_symmetry_hbond_refined 0.071 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_bond_other_d 0.006 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4162 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling