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Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A-K134A 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 lithium sulfate, 20% PEG 3350, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.97 58.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.825 α = 90 b = 115.825 β = 90 c = 119.316 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 2.95 50 91 0.084 25.3 8.7 29078 16029
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) 2.95 3.1 93.7 0.36 5.8 8.6 1613
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Used previously-determined structure THROUGHOUT PDB ENTRY 1L6M 2.95 50 15193 808 90.85 0.2595 0.25727 0.30292 0.2862 Used same set as previously-determined structure 34.763
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] 0.25 0.25 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.29 r_dihedral_angle_4_deg 17.971 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_1_deg 4.409 r_scangle_it 0.856 r_angle_refined_deg 0.829 r_angle_other_deg 0.792 r_mcangle_it 0.645 r_scbond_it 0.501 r_mcbond_it 0.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.29 r_dihedral_angle_4_deg 17.971 r_dihedral_angle_3_deg 14.689 r_dihedral_angle_1_deg 4.409 r_scangle_it 0.856 r_angle_refined_deg 0.829 r_angle_other_deg 0.792 r_mcangle_it 0.645 r_scbond_it 0.501 r_mcbond_it 0.345 r_nbtor_refined 0.177 r_nbd_other 0.173 r_nbd_refined 0.167 r_symmetry_vdw_refined 0.123 r_symmetry_vdw_other 0.123 r_xyhbond_nbd_refined 0.104 r_nbtor_other 0.077 r_symmetry_hbond_refined 0.058 r_chiral_restr 0.057 r_mcbond_other 0.033 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3865 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 7
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing