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Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant 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 0.2M Ammonium sulfate, 30% PEG4000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.9 57.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.908 α = 90 b = 114.908 β = 90 c = 118.832 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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 2.8 82.48 99 0.077 29.85 9.8 20269 20066
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 2.8 2.9 99.5 0.405 5.92 9.9 1955
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 1L6M 2.8 47.96 20269 19017 1026 99.02 0.25108 0.24827 0.2481 0.30397 0.2984 Used same set as previously-determined structure 31.185
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] -0.11 -0.11 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.074 r_dihedral_angle_4_deg 17.145 r_dihedral_angle_3_deg 14.554 r_dihedral_angle_1_deg 7.937 r_angle_refined_deg 0.941 r_scangle_it 0.885 r_angle_other_deg 0.792 r_mcangle_it 0.541 r_scbond_it 0.529 r_mcbond_it 0.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.074 r_dihedral_angle_4_deg 17.145 r_dihedral_angle_3_deg 14.554 r_dihedral_angle_1_deg 7.937 r_angle_refined_deg 0.941 r_scangle_it 0.885 r_angle_other_deg 0.792 r_mcangle_it 0.541 r_scbond_it 0.529 r_mcbond_it 0.286 r_nbd_other 0.18 r_nbtor_refined 0.177 r_nbd_refined 0.168 r_symmetry_vdw_refined 0.152 r_symmetry_vdw_other 0.125 r_symmetry_hbond_refined 0.109 r_xyhbond_nbd_refined 0.097 r_nbtor_other 0.078 r_chiral_restr 0.056 r_mcbond_other 0.03 r_metal_ion_refined 0.028 r_bond_other_d 0.007 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3911 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling