☰ Navigation Tabs
Crystal structure of Siderocalin (NGAL, Lipocalin 2) K134A mutant complexed with Ferric Enterobactin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 2.85 56.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.253 α = 90 b = 114.253 β = 90 c = 117.95 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 ADSC QUANTUM 210 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 2.6 50 99.9 0.123 12.4 13.9 24594
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) 2.6 2.7 99.9 0.39 4.9 14 2396
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1L6M 2.6 50 23297 1252 99.74 0.25725 0.25494 0.2513 0.29955 0.2924 Used same set as previously-determined structure 37.58
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 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.829 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 13.362 r_dihedral_angle_1_deg 5.071 r_scangle_it 1.487 r_scbond_it 1.026 r_angle_refined_deg 0.984 r_mcangle_it 0.827 r_angle_other_deg 0.788 r_mcbond_it 0.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.829 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 13.362 r_dihedral_angle_1_deg 5.071 r_scangle_it 1.487 r_scbond_it 1.026 r_angle_refined_deg 0.984 r_mcangle_it 0.827 r_angle_other_deg 0.788 r_mcbond_it 0.515 r_mcbond_other 0.311 r_nbd_refined 0.191 r_nbd_other 0.186 r_nbtor_refined 0.179 r_metal_ion_refined 0.163 r_xyhbond_nbd_refined 0.125 r_symmetry_vdw_other 0.109 r_symmetry_vdw_refined 0.103 r_symmetry_hbond_refined 0.101 r_nbtor_other 0.08 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_bond_other_d 0.006 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3902 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 145
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing