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Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric 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 4.5 291 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 291K
Crystal Properties Matthews coefficient Solvent content 3.21 61.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.421 α = 90 b = 115.421 β = 90 c = 118.801 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 0.055 31.5 7.9 68321 36375 50.4
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 0.39 5.09 6.8 3562
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 THROUGHOUT 1L6M 2.3 40.79 32869 3443 99.8 0.25827 0.25562 0.2576 0.28376 0.2858 RANDOM 39.229
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] 0.06 0.06 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.957 r_dihedral_angle_4_deg 15.877 r_dihedral_angle_3_deg 12.846 r_dihedral_angle_1_deg 4.865 r_scangle_it 1.247 r_angle_refined_deg 0.925 r_angle_other_deg 0.822 r_scbond_it 0.747 r_mcangle_it 0.694 r_mcbond_it 0.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.957 r_dihedral_angle_4_deg 15.877 r_dihedral_angle_3_deg 12.846 r_dihedral_angle_1_deg 4.865 r_scangle_it 1.247 r_angle_refined_deg 0.925 r_angle_other_deg 0.822 r_scbond_it 0.747 r_mcangle_it 0.694 r_mcbond_it 0.366 r_nbd_other 0.176 r_nbtor_refined 0.171 r_metal_ion_refined 0.168 r_nbd_refined 0.165 r_symmetry_vdw_other 0.118 r_symmetry_hbond_refined 0.11 r_symmetry_vdw_refined 0.101 r_xyhbond_nbd_refined 0.092 r_nbtor_other 0.078 r_chiral_restr 0.063 r_mcbond_other 0.034 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 3683 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 99
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing