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Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Fe-TrenCam2-hopo
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 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 2.88 57.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.802 α = 90 b = 114.802 β = 90 c = 118.352 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 3.2 50 100 0.135 22.15 13.6 25061 13667
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) 3.2 3.3 99.8 0.44 6.9 13.7 1330
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 PDB ENTRY 1L6M 3.2 48 12377 1214 99.71 0.22148 0.21647 0.2178 0.27186 0.2642 Used same set as previously-determined structure 25.926
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] -0.28 -0.28 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.647 r_dihedral_angle_4_deg 18.806 r_dihedral_angle_3_deg 18.289 r_dihedral_angle_1_deg 9.761 r_angle_refined_deg 2.953 r_scangle_it 1.449 r_angle_other_deg 1.13 r_scbond_it 0.936 r_mcangle_it 0.802 r_mcbond_it 0.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.647 r_dihedral_angle_4_deg 18.806 r_dihedral_angle_3_deg 18.289 r_dihedral_angle_1_deg 9.761 r_angle_refined_deg 2.953 r_scangle_it 1.449 r_angle_other_deg 1.13 r_scbond_it 0.936 r_mcangle_it 0.802 r_mcbond_it 0.438 r_symmetry_vdw_other 0.215 r_nbd_refined 0.205 r_nbd_other 0.202 r_nbtor_refined 0.193 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.145 r_nbtor_other 0.08 r_metal_ion_refined 0.071 r_chiral_restr 0.067 r_mcbond_other 0.05 r_bond_refined_d 0.016 r_bond_other_d 0.007 r_gen_planes_refined 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3920 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 159
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing