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Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 4-methyl-catechol
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 4.5 293 1.0-1.4M Ammonium sulfate, 50 mM Sodium Chloride, 200 mM Lithium Sulfate, 100 mM Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.19 61.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.904 α = 90 b = 114.904 β = 90 c = 119.164 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 2008-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 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 2.3 50 99.9 0.048 25 8 67567 35984 45.5
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) 2.3 2.38 100 0.4 5.39 7.8 3519
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 2.3 40.62 32519 3403 99.85 0.24825 0.24398 0.2458 0.28973 0.2891 RANDOM 35.513
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] 0.22 0.22 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.356 r_dihedral_angle_4_deg 21.478 r_dihedral_angle_3_deg 15.069 r_dihedral_angle_1_deg 5.172 r_scangle_it 1.257 r_angle_refined_deg 0.941 r_angle_other_deg 0.791 r_mcangle_it 0.784 r_scbond_it 0.758 r_mcbond_it 0.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.356 r_dihedral_angle_4_deg 21.478 r_dihedral_angle_3_deg 15.069 r_dihedral_angle_1_deg 5.172 r_scangle_it 1.257 r_angle_refined_deg 0.941 r_angle_other_deg 0.791 r_mcangle_it 0.784 r_scbond_it 0.758 r_mcbond_it 0.418 r_metal_ion_refined 0.236 r_nbd_other 0.181 r_nbtor_refined 0.176 r_nbd_refined 0.163 r_symmetry_vdw_other 0.144 r_symmetry_hbond_refined 0.113 r_symmetry_vdw_refined 0.106 r_xyhbond_nbd_refined 0.094 r_nbtor_other 0.08 r_chiral_restr 0.061 r_mcbond_other 0.038 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3901 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing